diff --git a/README.md b/README.md index fa97335..9c8d8fc 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,9 @@ It compares the execution results of [nf-core/rnaseq v3.7](https://nf-co.re/rnas ```bash $ tonkaz ./tests/example_crate/rnaseq_1st.json ./tests/example_crate/rnaseq_2nd.json + +# Example output: +$ cat ./tests/comparison_results/rnaseq_same_env.log ``` We provide various examples in the [tests/README.md](./tests/README.md). diff --git a/tests/README.md b/tests/README.md index ca362cb..b597764 100644 --- a/tests/README.md +++ b/tests/README.md @@ -2,9 +2,13 @@ This directory contains tests for `Tonkaz`. -These test data are generated using [`sapporo-wes/sapporo-service`](https://github.com/sapporo-wes/sapporo-service) and [`sapporo-wes/yevis-cli`](https://github.com/sapporo-wes/yevis-cli). +These test data are generated using [`sapporo-wes/sapporo-service`](https://github.com/sapporo-wes/sapporo-service), [`sapporo-wes/yevis-cli`](https://github.com/sapporo-wes/yevis-cli) and Tonkaz. -Also, please check [sapporo-wes/test-workflow](https://github.com/sapporo-wes/test-workflow). +The procedure of generating each data is as follows: + +``` +workflow -- (Sapporo-service/Yevis) --> execution_results + ro_crate -- (Tonkaz) --> comparison_results +``` ## Run tests @@ -12,29 +16,50 @@ Several combinations of crates are available as follows: ```bash # GATK (Linux, 1st) <-> GATK (Linux, 2nd) +# Use case: Same environment +# Result: ./comparison_results/gatk_same_env.log $ deno test -A ./tests/gatk_test.ts # GATK (Linux) <-> GATK (Mac) +# Use case: Different environment +# Result: ./comparison_results/gatk_diff_env.log $ deno test -A ./tests/gatk_mac_test.ts # JGA (Linux, 1st) <-> JGA (Linux, 2nd) +# Use case: Same environment +# Result: ./comparison_results/jga_same_env.log $ deno test -A ./tests/jga_test.ts # JGA (Linux) <-> JGA (Mac) +# Use case: Different environment +# Result: ./comparison_results/jga_diff_env.log $ deno test -A ./tests/jga_mac_test.ts # RNA-seq (Linux, 1st) <-> RNA-seq (Linux, 2nd) +# Use case: Same environment +# Result: ./comparison_results/rnaseq_same_env.log $ deno test -A ./tests/rnaseq_test.ts # RNA-seq (Linux) <-> RNA-seq (Mac) +# Use case: Different environment +# Result: ./comparison_results/rnaseq_diff_env.log $ deno test -A ./tests/rnaseq_mac_test.ts # RNA-seq (Linux, 1st) <-> RNA-seq (Linux, v3.6) +# Use case: Different version +# Result: ./comparison_results/rnaseq_diff_ver.log $ deno test -A ./tests/rnaseq_v3.6_test.ts # RNA-seq (Linux, 1st) <-> RNA-seq (Linux, small) +# Use case: Missing dataset +# Result: ./comparison_results/rnaseq_missing_data.log $ deno test -A ./tests/rnaseq_small_test.ts +# RNA-seq (Linux, 1st) <-> RNA-seq (Linux, small) +# Use case: All files +# Result: ./comparison_results/rnaseq_all_files.log +$ deno test -A ./tests/rnaseq_all_files_test.ts + # RNA-seq (Linux, with yevis) <-> RNA-seq (Linux, only sapporo) $ deno test -A ./tests/rnaseq_only_sapporo_test.ts @@ -44,7 +69,9 @@ $ deno test -A ./tests/trimming_mac_test.ts ## About test data -The json files contained in [`example_crate`](./example_crate) are generated using [`sapporo-wes/sapporo-service`](https://github.com/sapporo-wes/sapporo-service) and [`sapporo-wes/yevis-cli`](https://github.com/sapporo-wes/yevis-cli). +The raw data of workflow execution results are stored in [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7098337.svg)](https://doi.org/10.5281/zenodo.7098337). + +The crate files contained in [`example_crate`](./example_crate): ``` example_crate/ @@ -66,7 +93,7 @@ example_crate/ ### Executed environment -About the environment in which the crate was generated. +About the environment in which these crates were generated. | Field | Linux env | Mac Apple silicon env | | ----------------------- | ------------------------------------------ | --------------------- | @@ -97,6 +124,24 @@ Executed as follows: $ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_gatk-workflows_mitochondria-pipeline.yml ``` +### JGA + +- Crate: + - [`jga_1st.json`](./example_crate/jga_1st.json) + - Crate generated on `Linux` environment. (1st execution) + - [`jga_2nd.json`](./example_crate/jga_2nd.json) + - Crate generated on `Linux` environment. (2nd execution (same settings)) + - [`jga_mac.json`](./example_crate/jga_mac.json) + - Crate generated on `Mac Apple silicon` environment. + +See https://github.com/sapporo-wes/test-workflow#biosciencedbcjga-analysis---per-sample-workflow for more details about the executed workflow. + +Executed as follows: + +```bash +$ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_jga-workflow_per-sample.yml +``` + ### RNA-seq - Crate: @@ -131,24 +176,6 @@ $ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test $ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_nf-core_rnaseq_v3.6.yml ``` -### JGA - -- Crate: - - [`jga_1st.json`](./example_crate/jga_1st.json) - - Crate generated on `Linux` environment. (1st execution) - - [`jga_2nd.json`](./example_crate/jga_2nd.json) - - Crate generated on `Linux` environment. (2nd execution (same settings)) - - [`jga_mac.json`](./example_crate/jga_mac.json) - - Crate generated on `Mac Apple silicon` environment. - -See https://github.com/sapporo-wes/test-workflow#biosciencedbcjga-analysis---per-sample-workflow for more details about the executed workflow. - -Executed as follows: - -```bash -$ yevis test --fetch-ro-crate https://raw.githubusercontent.com/sapporo-wes/test-workflow/main/yevis-metadata_jga-workflow_per-sample.yml -``` - ### Trimming - Crate: diff --git a/tests/comparison_results/gatk_diff_env.log b/tests/comparison_results/gatk_diff_env.log new file mode 100644 index 0000000..efdc1b0 --- /dev/null +++ b/tests/comparison_results/gatk_diff_env.log @@ -0,0 +1,69 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/gatk_1st.json + Crate2: ./tests/example_crate/gatk_mac.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | GATK workf ... Mitochondria Pipeline | GATK workf ... Mitochondria Pipeline | +| WF ID | 68c32f9c-bdaa-420c-879c-90b40d8bc4d5 | 68c32f9c-bdaa-420c-879c-90b40d8bc4d5 | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Workflow Description Language | Workflow Description Language | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | cromwell | cromwell | +| WF Eng Version | 80 | 80 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE  | EXECUTOR_ERROR  | +| ExitCode | 0  | 1  | +| Start Time | 2022-09-08 09:30:03 | 2022-09-14 05:42:22 | +| End Time | 2022-09-08 09:58:32 | 2022-09-14 05:44:11 | +| Duration | 28m 29s | 1m 49s | +| # Attachments | 2 files | 2 files | +| # Intermediate | 314 files  | 12 files  | +| # Outputs | 13 files (5 EDAM-assigned files)  | 0 files (0 EDAM-assigned files)  | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 0/0 files) + +=== Level2 ⭐⭐ (Similar Features, 0/0 files) + +=== Level1 ⭐ (Different Features, 0/0 files) + +=== Level0 (Not Found, Crate1: 5 files, Crate2: 0 files) + + - Only in Crate1: + + - outputs/G97753.NA12878.bam + - outputs/G97753.NA12878.final.split.vcf + - outputs/G97753.NA12878.realigned.bam + - outputs/G97753.NA12878.vcf + - outputs/splitAndPassOnly.vcf + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 0 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 0 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 5 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/gatk_same_env.log b/tests/comparison_results/gatk_same_env.log new file mode 100644 index 0000000..b9e9068 --- /dev/null +++ b/tests/comparison_results/gatk_same_env.log @@ -0,0 +1,108 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/gatk_1st.json + Crate2: ./tests/example_crate/gatk_2nd.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | GATK workf ... Mitochondria Pipeline | GATK workf ... Mitochondria Pipeline | +| WF ID | 68c32f9c-bdaa-420c-879c-90b40d8bc4d5 | 68c32f9c-bdaa-420c-879c-90b40d8bc4d5 | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Workflow Description Language | Workflow Description Language | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | cromwell | cromwell | +| WF Eng Version | 80 | 80 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-08 09:30:03 | 2022-09-08 08:59:34 | +| End Time | 2022-09-08 09:58:32 | 2022-09-08 09:26:25 | +| Duration | 28m 29s | 26m 51s | +| # Attachments | 2 files | 2 files | +| # Intermediate | 314 files | 314 files | +| # Outputs | 13 files (5 EDAM-assigned files) | 13 files (5 EDAM-assigned files) | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 0/5 files) + +=== Level2 ⭐⭐ (Similar Features, 5/5 files) + + - G97753.NA12878.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 147.78 MB (154962060)  | 147.78 MB (154962147)  | + | Total Reads | 2349886 | 2349886 | + | # Mapped | 2349886 (100.00%) | 2349886 (100.00%) | + | # Duplicate | 719878 (30.63%) | 719878 (30.63%) | + '--------------------------------------------------------------------' + + - G97753.NA12878.final.split.vcf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.51 KB (18955)  | 18.51 KB (18953)  | + | Line Count | 107 | 107 | + '--------------------------------------------------------------------' + + - G97753.NA12878.realigned.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 98.46 MB (103241649)  | 98.46 MB (103241732)  | + | Total Reads | 2361236 | 2361236 | + | # Mapped | 2361223 (100.00%) | 2361223 (100.00%) | + | # Duplicate | 723304 (30.63%) | 723304 (30.63%) | + '--------------------------------------------------------------------' + + - G97753.NA12878.vcf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 24.48 KB (25069)  | 24.48 KB (25063)  | + | Line Count | 99 | 99 | + '--------------------------------------------------------------------' + + - splitAndPassOnly.vcf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.85 KB (16229)  | 15.85 KB (16228)  | + | Line Count | 96 | 96 | + | Variant Count | 18 | 18 | + | SNPs Count | 16 | 16 | + | Indels Count | 2 | 2 | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 0/5 files) + +=== Level0 (Not Found, Crate1: 0 files, Crate2: 0 files) + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 0 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 5 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 0 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/jga_diff_env.log b/tests/comparison_results/jga_diff_env.log new file mode 100644 index 0000000..7ee674f --- /dev/null +++ b/tests/comparison_results/jga_diff_env.log @@ -0,0 +1,68 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/jga_1st.json + Crate2: ./tests/example_crate/jga_mac.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | jga-analysis per-sample workflow | jga-analysis per-sample workflow | +| WF ID | 579bbccf-ff06-4c5f-98cb-d7a2dc73eca8 | 579bbccf-ff06-4c5f-98cb-d7a2dc73eca8 | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Common Workflow Language | Common Workflow Language | +| WF Type Ver | v1.1 | v1.1 | +| WF Eng Name | cwltool | cwltool | +| WF Eng Version | 3.1.20220628170238 | 3.1.20220628170238 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | test_1 | test_1 | +| Run State | COMPLETE  | CANCELED  | +| ExitCode | 0  | 138  | +| Start Time | 2022-09-10 13:33:40 | 2022-09-15 06:49:26 | +| End Time | 2022-09-10 15:03:05 | 2022-09-15 10:28:54 | +| Duration | 1h 29m 25s | 3h 39m 28s | +| # Attachments | 0 files | 0 files | +| # Intermediate | 0 files | 0 files | +| # Outputs | 48 files (4 EDAM-assigned files)  | 0 files (0 EDAM-assigned files)  | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 0/0 files) + +=== Level2 ⭐⭐ (Similar Features, 0/0 files) + +=== Level1 ⭐ (Different Features, 0/0 files) + +=== Level0 (Not Found, Crate1: 4 files, Crate2: 0 files) + + - Only in Crate1: + + - outputs/NA19023.autosome_PAR_ploidy_2.g.vcf.gz + - outputs/NA19023.chrX_nonPAR_ploidy_1.g.vcf.gz + - outputs/NA19023.chrX_nonPAR_ploidy_2.g.vcf.gz + - outputs/NA19023.chrY_nonPAR_ploidy_1.g.vcf.gz + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 0 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 0 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 4 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/jga_same_env.log b/tests/comparison_results/jga_same_env.log new file mode 100644 index 0000000..0eab84e --- /dev/null +++ b/tests/comparison_results/jga_same_env.log @@ -0,0 +1,101 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/jga_1st.json + Crate2: ./tests/example_crate/jga_2nd.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | jga-analysis per-sample workflow | jga-analysis per-sample workflow | +| WF ID | 579bbccf-ff06-4c5f-98cb-d7a2dc73eca8 | 579bbccf-ff06-4c5f-98cb-d7a2dc73eca8 | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Common Workflow Language | Common Workflow Language | +| WF Type Ver | v1.1 | v1.1 | +| WF Eng Name | cwltool | cwltool | +| WF Eng Version | 3.1.20220628170238 | 3.1.20220628170238 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | test_1 | test_1 | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-10 13:33:40 | 2022-09-10 20:40:42 | +| End Time | 2022-09-10 15:03:05 | 2022-09-10 22:09:08 | +| Duration | 1h 29m 25s | 1h 28m 26s | +| # Attachments | 0 files | 0 files | +| # Intermediate | 0 files | 0 files | +| # Outputs | 48 files (4 EDAM-assigned files) | 48 files (4 EDAM-assigned files) | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 0/4 files) + +=== Level2 ⭐⭐ (Similar Features, 4/4 files) + + - NA19023.autosome_PAR_ploidy_2.g.vcf.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 33.59 KB (34397)  | 33.59 KB (34398)  | + | Variant Count | 1061 | 1061 | + | SNPs Count | 14 | 14 | + | Indels Count | 1 | 1 | + '--------------------------------------------------------------------' + + - NA19023.chrX_nonPAR_ploidy_1.g.vcf.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 23.84 KB (24408)  | 23.84 KB (24409)  | + | Variant Count | 2 | 2 | + | SNPs Count | 0 | 0 | + | Indels Count | 0 | 0 | + '--------------------------------------------------------------------' + + - NA19023.chrX_nonPAR_ploidy_2.g.vcf.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 24.03 KB (24602)  | 24.02 KB (24601)  | + | Variant Count | 2 | 2 | + | SNPs Count | 0 | 0 | + | Indels Count | 0 | 0 | + '--------------------------------------------------------------------' + + - NA19023.chrY_nonPAR_ploidy_1.g.vcf.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 24.35 KB (24931)  | 24.35 KB (24935)  | + | Variant Count | 42 | 42 | + | SNPs Count | 4 | 4 | + | Indels Count | 0 | 0 | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 0/4 files) + +=== Level0 (Not Found, Crate1: 0 files, Crate2: 0 files) + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 0 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 4 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 0 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/rnaseq_all_files.log b/tests/comparison_results/rnaseq_all_files.log new file mode 100644 index 0000000..c3d594c --- /dev/null +++ b/tests/comparison_results/rnaseq_all_files.log @@ -0,0 +1,2968 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/rnaseq_1st.json + Crate2: ./tests/example_crate/rnaseq_2nd.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | nf-core - rnaseq | nf-core - rnaseq | +| WF ID | 20da6ea5-de91-4973-ac20-216882357a0d | 20da6ea5-de91-4973-ac20-216882357a0d | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Nextflow | Nextflow | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | nextflow | nextflow | +| WF Eng Version | 22.04.4 | 22.04.4 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-08 06:28:11 | 2022-09-08 06:08:01 | +| End Time | 2022-09-08 06:45:53 | 2022-09-08 06:25:56 | +| Duration | 17m 42s | 17m 55s | +| # Attachments | 147 files | 147 files | +| # Intermediate | 3342 files | 3342 files | +| # Outputs | 872 files (25 EDAM-assigned files) | 872 files (25 EDAM-assigned files) | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the output files of Crate1 and Crate2. + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 557/864 files) + + - bbsplit/RAP1_IAA_30M_REP1.stats.txt + - bbsplit/RAP1_UNINDUCED_REP1.stats.txt + - bbsplit/RAP1_UNINDUCED_REP2.stats.txt + - bbsplit/WT_REP1.stats.txt + - fastqc/RAP1_IAA_30M_REP1_1_fastqc.html + - fastqc/RAP1_IAA_30M_REP1_2_fastqc.html + - fastqc/RAP1_UNINDUCED_REP1_fastqc.html + - fastqc/RAP1_UNINDUCED_REP2_fastqc.html + - fastqc/WT_REP1_1_fastqc.html + - fastqc/WT_REP1_2_fastqc.html + - fastqc/WT_REP2_1_fastqc.html + - fastqc/WT_REP2_2_fastqc.html + - multiqc/star_salmon/multiqc_data/mqc_cutadapt_filtered_reads_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_cutadapt_trimmed_sequences_plot_3_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_adapter_content_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_overrepresented_sequences_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_overrepresented_sequences_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_base_n_content_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_base_n_content_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_per_sequence_quality_scores_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_sequence_counts_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_sequence_counts_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot-2_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_sequence_duplication_levels_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_fastqc_sequence_length_distribution_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_featurecounts_biotype_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_picard_deduplication_1.txt + - multiqc/star_salmon/multiqc_data/mqc_preseq_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_qualimap_gene_coverage_profile_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_qualimap_gene_coverage_profile_Normalised.txt + - multiqc/star_salmon/multiqc_data/mqc_qualimap_genomic_origin_1.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_infer_experiment_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_inner_distance_plot_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_inner_distance_plot_Percentages.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_junction_annotation_junctions_plot_Events.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_junction_annotation_junctions_plot_Junctions.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_read_distribution_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_rseqc_read_dups_plot_1.txt + - multiqc/star_salmon/multiqc_data/mqc_samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_samtools-idxstats-mapped-reads-plot_Raw_Counts.txt + - multiqc/star_salmon/multiqc_data/mqc_samtools_alignment_plot_1.txt + - multiqc/star_salmon/multiqc_data/multiqc_cutadapt.txt + - multiqc/star_salmon/multiqc_data/multiqc_fastqc.txt + - multiqc/star_salmon/multiqc_data/multiqc_fastqc_1.txt + - multiqc/star_salmon/multiqc_data/multiqc_picard_dups.txt + - multiqc/star_salmon/multiqc_data/multiqc_rseqc_bam_stat.txt + - multiqc/star_salmon/multiqc_data/multiqc_rseqc_infer_experiment.txt + - multiqc/star_salmon/multiqc_data/multiqc_rseqc_junction_annotation.txt + - multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt + - multiqc/star_salmon/multiqc_data/multiqc_samtools_flagstat.txt + - multiqc/star_salmon/multiqc_data/multiqc_samtools_idxstats.txt + - multiqc/star_salmon/multiqc_data/multiqc_samtools_stats.txt + - multiqc/star_salmon/multiqc_plots/png/mqc_cutadapt_filtered_reads_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_cutadapt_filtered_reads_plot_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_cutadapt_trimmed_sequences_plot_3_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_cutadapt_trimmed_sequences_plot_3_Obs_Exp.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_adapter_content_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_overrepresented_sequences_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_overrepresented_sequences_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_base_n_content_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_base_n_content_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_base_sequence_quality_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_base_sequence_quality_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_gc_content_plot_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_gc_content_plot_Percentages.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_quality_scores_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_per_sequence_quality_scores_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_counts_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_counts_plot-2_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_counts_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_counts_plot_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_duplication_levels_plot-2_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_duplication_levels_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_fastqc_sequence_length_distribution_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_featurecounts_biotype_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_featurecounts_biotype_plot_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_picard_deduplication_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_picard_deduplication_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_preseq_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_qualimap_gene_coverage_profile_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_qualimap_gene_coverage_profile_Normalised.png + - multiqc/star_salmon/multiqc_plots/png/mqc_qualimap_genomic_origin_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_qualimap_genomic_origin_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_infer_experiment_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_inner_distance_plot_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_inner_distance_plot_Percentages.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_annotation_junctions_plot_Events.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_annotation_junctions_plot_Events_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_annotation_junctions_plot_Junctions.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_annotation_junctions_plot_Junctions_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_read_distribution_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_read_distribution_plot_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_read_dups_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_samtools-idxstats-mapped-reads-plot_Normalised_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_samtools-idxstats-mapped-reads-plot_Raw_Counts.png + - multiqc/star_salmon/multiqc_plots/png/mqc_samtools_alignment_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_samtools_alignment_plot_1_pc.png + - multiqc/star_salmon/multiqc_plots/png/mqc_star_alignment_plot_1.png + - multiqc/star_salmon/multiqc_plots/png/mqc_star_alignment_plot_1_pc.png + - pipeline_info/samplesheet.valid.csv + - pipeline_info/software_versions.yml + - salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv + - salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz + - salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz + - salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz + - salmon/RAP1_IAA_30M_REP1/cmd_info.json + - salmon/RAP1_IAA_30M_REP1/lib_format_counts.json + - salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv + - salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz + - salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz + - salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz + - salmon/RAP1_UNINDUCED_REP1/cmd_info.json + - salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt + - salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json + - salmon/RAP1_UNINDUCED_REP1/quant.genes.sf + - salmon/RAP1_UNINDUCED_REP1/quant.sf + - salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv + - salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz + - salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz + - salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz + - salmon/RAP1_UNINDUCED_REP2/cmd_info.json + - salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt + - salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json + - salmon/RAP1_UNINDUCED_REP2/quant.genes.sf + - salmon/RAP1_UNINDUCED_REP2/quant.sf + - salmon/WT_REP1/aux_info/ambig_info.tsv + - salmon/WT_REP1/aux_info/expected_bias.gz + - salmon/WT_REP1/aux_info/observed_bias.gz + - salmon/WT_REP1/aux_info/observed_bias_3p.gz + - salmon/WT_REP1/cmd_info.json + - salmon/WT_REP1/lib_format_counts.json + - salmon/WT_REP2/aux_info/ambig_info.tsv + - salmon/WT_REP2/aux_info/expected_bias.gz + - salmon/WT_REP2/aux_info/observed_bias.gz + - salmon/WT_REP2/aux_info/observed_bias_3p.gz + - salmon/WT_REP2/cmd_info.json + - salmon/WT_REP2/lib_format_counts.json + - salmon/deseq2_qc/R_sessionInfo.log + - salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt + - salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt + - salmon/deseq2_qc/size_factors/WT_REP1.txt + - salmon/deseq2_qc/size_factors/WT_REP2.txt + - salmon/salmon.merged.gene_counts.tsv + - salmon/salmon.merged.transcript_counts.tsv + - salmon/salmon_tx2gene.tsv + - star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv + - star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz + - star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz + - star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz + - star_salmon/RAP1_IAA_30M_REP1/cmd_info.json + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz + - star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json + - star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz + - star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json + - star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt + - star_salmon/WT_REP1/aux_info/ambig_info.tsv + - star_salmon/WT_REP1/aux_info/expected_bias.gz + - star_salmon/WT_REP1/aux_info/observed_bias.gz + - star_salmon/WT_REP1/aux_info/observed_bias_3p.gz + - star_salmon/WT_REP1/cmd_info.json + - star_salmon/WT_REP2/aux_info/ambig_info.tsv + - star_salmon/WT_REP2/aux_info/expected_bias.gz + - star_salmon/WT_REP2/aux_info/observed_bias.gz + - star_salmon/WT_REP2/aux_info/observed_bias_3p.gz + - star_salmon/WT_REP2/cmd_info.json + - star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig + - star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig + - star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig + - star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig + - star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig + - star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig + - star_salmon/bigwig/WT_REP1.forward.bigWig + - star_salmon/bigwig/WT_REP1.reverse.bigWig + - star_salmon/bigwig/WT_REP2.forward.bigWig + - star_salmon/bigwig/WT_REP2.reverse.bigWig + - star_salmon/deseq2_qc/R_sessionInfo.log + - star_salmon/deseq2_qc/deseq2.dds.RData + - star_salmon/deseq2_qc/deseq2.pca.vals.txt + - star_salmon/deseq2_qc/deseq2.sample.dists.txt + - star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt + - star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt + - star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt + - star_salmon/deseq2_qc/size_factors/WT_REP1.txt + - star_salmon/deseq2_qc/size_factors/WT_REP2.txt + - star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData + - star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt + - star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt + - star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt + - star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt + - star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt + - star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt + - star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt + - star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt + - star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt + - star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt + - star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv + - star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv + - star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt + - star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary + - star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv + - star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv + - star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt + - star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary + - star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv + - star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv + - star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt + - 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star_salmon/stringtie/WT_REP2.coverage.gtf + - star_salmon/stringtie/WT_REP2.gene.abundance.txt + - star_salmon/stringtie/WT_REP2.transcripts.gtf + - trimgalore/fastqc/RAP1_IAA_30M_REP1_1_val_1_fastqc.html + - trimgalore/fastqc/RAP1_IAA_30M_REP1_2_val_2_fastqc.html + - trimgalore/fastqc/RAP1_UNINDUCED_REP1_trimmed_fastqc.html + - trimgalore/fastqc/RAP1_UNINDUCED_REP2_trimmed_fastqc.html + - trimgalore/fastqc/WT_REP1_1_val_1_fastqc.html + - trimgalore/fastqc/WT_REP1_2_val_2_fastqc.html + - trimgalore/fastqc/WT_REP2_1_val_1_fastqc.html + - trimgalore/fastqc/WT_REP2_2_val_2_fastqc.html + +=== Level2 ⭐⭐ (Similar Features, 306/864 files) + + - bbsplit/WT_REP2.stats.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 241.00 B (241) | 241.00 B (241) | + | Line Count | 3 | 3 | + '--------------------------------------------------------------------' + + - 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fastqc/RAP1_UNINDUCED_REP2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 355.12 KB (363643) | 355.12 KB (363643) | + '--------------------------------------------------------------------' + + - fastqc/WT_REP1_1_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 357.86 KB (366448) | 357.86 KB (366448) | + '--------------------------------------------------------------------' + + - fastqc/WT_REP1_2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 348.23 KB (356587) | 348.23 KB (356587) | + '--------------------------------------------------------------------' + + - fastqc/WT_REP2_1_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 353.13 KB (361601) | 353.13 KB (361601) | + '--------------------------------------------------------------------' + + - fastqc/WT_REP2_2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 346.20 KB (354509) | 346.20 KB (354509) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/mqc_rseqc_junction_saturation_plot_All_Junctions.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 690.00 B (690)  | 692.00 B (692)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/mqc_rseqc_junction_saturation_plot_Known_Junctions.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 581.00 B (581) | 581.00 B (581) | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/mqc_rseqc_junction_saturation_plot_Novel_Junctions.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 688.00 B (688)  | 687.00 B (687)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/mqc_salmon_plot_1.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 29.03 KB (29729)  | 29.05 KB (29744)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/mqc_star_alignment_plot_1.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 342.00 B (342) | 342.00 B (342) | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/multiqc.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 25.15 KB (25753) | 25.15 KB (25753) | + | Line Count | 137 | 137 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/multiqc_data.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.96 MB (2058523)  | 1.96 MB (2058544)  | + | Line Count | 57803 | 57803 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.59 KB (3674)  | 3.59 KB (3675)  | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/multiqc_salmon.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.59 KB (4697)  | 4.59 KB (4699)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_data/multiqc_sources.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 23.19 KB (23742) | 23.19 KB (23742) | + | Line Count | 103 | 103 | + '--------------------------------------------------------------------' + + - 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multiqc/star_salmon/multiqc_plots/pdf/mqc_cutadapt_trimmed_sequences_plot_3_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.44 KB (19907) | 19.44 KB (19907) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 20.43 KB (20921) | 20.43 KB (20921) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_adapter_content_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.08 KB (19539) | 19.08 KB (19539) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_overrepresented_sequences_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 17.10 KB (17510) | 17.10 KB (17510) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_overrepresented_sequences_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 17.11 KB (17518) | 17.11 KB (17518) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_base_n_content_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.48 KB (18920) | 18.48 KB (18920) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_base_n_content_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.23 KB (18663) | 18.23 KB (18663) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_base_sequence_quality_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.23 KB (19691) | 19.23 KB (19691) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_base_sequence_quality_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.23 KB (19691) | 19.23 KB (19691) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.71 KB (19161) | 18.71 KB (19161) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.32 KB (19784) | 19.32 KB (19784) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_gc_content_plot_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.75 KB (19195) | 18.75 KB (19195) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_gc_content_plot_Percentages.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 19.24 KB (19697) | 19.24 KB (19697) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_quality_scores_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.84 KB (17247) | 16.84 KB (17247) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_per_sequence_quality_scores_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.91 KB (17316) | 16.91 KB (17316) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_counts_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.66 KB (16039) | 15.66 KB (16039) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_counts_plot-2_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.13 KB (16514) | 16.13 KB (16514) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_counts_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.60 KB (15977) | 15.60 KB (15977) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_counts_plot_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.13 KB (16520) | 16.13 KB (16520) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_duplication_levels_plot-2_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.37 KB (18813) | 18.37 KB (18813) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_duplication_levels_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.37 KB (18807) | 18.37 KB (18807) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_fastqc_sequence_length_distribution_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.87 KB (19319) | 18.87 KB (19319) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_featurecounts_biotype_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.08 KB (15443) | 15.08 KB (15443) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_featurecounts_biotype_plot_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.56 KB (15938) | 15.56 KB (15938) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_picard_deduplication_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.09 KB (14427) | 14.09 KB (14427) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_picard_deduplication_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.08 KB (15438) | 15.08 KB (15438) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_preseq_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 17.17 KB (17587) | 17.17 KB (17587) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_qualimap_gene_coverage_profile_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 21.29 KB (21804) | 21.29 KB (21804) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_qualimap_gene_coverage_profile_Normalised.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 21.28 KB (21795) | 21.28 KB (21795) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_qualimap_genomic_origin_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.86 KB (16236) | 15.86 KB (16236) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_qualimap_genomic_origin_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.85 KB (17252) | 16.85 KB (17252) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_infer_experiment_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.85 KB (15203) | 14.85 KB (15203) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_inner_distance_plot_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.49 KB (15857) | 15.49 KB (15857) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_inner_distance_plot_Percentages.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.47 KB (15841) | 15.47 KB (15841) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_annotation_junctions_plot_Events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.81 KB (15164) | 14.81 KB (15164) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_annotation_junctions_plot_Events_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.73 KB (15080) | 14.73 KB (15080) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_annotation_junctions_plot_Junctions.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.83 KB (15189) | 14.83 KB (15189) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_annotation_junctions_plot_Junctions_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.71 KB (15064) | 14.71 KB (15064) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_saturation_plot_All_Junctions.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.49 KB (15865)  | 15.49 KB (15861)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_saturation_plot_Known_Junctions.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.43 KB (15799)  | 15.44 KB (15811)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_junction_saturation_plot_Novel_Junctions.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.51 KB (15883)  | 15.47 KB (15838)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_read_distribution_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.66 KB (16032) | 15.66 KB (16032) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_read_distribution_plot_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.07 KB (16451) | 16.07 KB (16451) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_rseqc_read_dups_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 18.07 KB (18501) | 18.07 KB (18501) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_salmon_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 23.76 KB (24329)  | 23.75 KB (24316)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_samtools-idxstats-mapped-reads-plot_Normalised_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 15.85 KB (16231) | 15.85 KB (16231) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.83 KB (17231) | 16.83 KB (17231) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_samtools-idxstats-mapped-reads-plot_Raw_Counts.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.95 KB (15313) | 14.95 KB (15313) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_samtools_alignment_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 13.81 KB (14142) | 13.81 KB (14142) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_samtools_alignment_plot_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.80 KB (15154) | 14.80 KB (15154) | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_star_alignment_plot_1.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.13 KB (16517)  | 16.13 KB (16516)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/pdf/mqc_star_alignment_plot_1_pc.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 16.58 KB (16974)  | 16.58 KB (16973)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_saturation_plot_All_Junctions.png + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 50.50 KB (51710)  | 49.89 KB (51092)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_saturation_plot_Known_Junctions.png + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 26.80 KB (27447)  | 26.84 KB (27481)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/png/mqc_rseqc_junction_saturation_plot_Novel_Junctions.png + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 50.45 KB (51662)  | 50.08 KB (51285)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/png/mqc_salmon_plot_1.png + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 47.84 KB (48985)  | 47.88 KB (49034)  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_cutadapt_filtered_reads_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 30.42 KB (31150) | 30.42 KB (31150) | + | Line Count | 1203 | 1203 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_cutadapt_filtered_reads_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 30.80 KB (31540) | 30.80 KB (31540) | + | Line Count | 1241 | 1241 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_cutadapt_trimmed_sequences_plot_3_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 55.10 KB (56421) | 55.10 KB (56421) | + | Line Count | 2054 | 2054 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 58.23 KB (59632) | 58.23 KB (59632) | + | Line Count | 2164 | 2164 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_adapter_content_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 59.04 KB (60457) | 59.04 KB (60457) | + | Line Count | 2115 | 2115 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_overrepresented_sequences_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 40.88 KB (41859) | 40.88 KB (41859) | + | Line Count | 1596 | 1596 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_overrepresented_sequences_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 40.88 KB (41859) | 40.88 KB (41859) | + | Line Count | 1596 | 1596 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_base_n_content_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 46.26 KB (47374) | 46.26 KB (47374) | + | Line Count | 1842 | 1842 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_base_n_content_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 46.30 KB (47410) | 46.30 KB (47410) | + | Line Count | 1842 | 1842 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_base_sequence_quality_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 46.24 KB (47351) | 46.24 KB (47351) | + | Line Count | 1861 | 1861 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_base_sequence_quality_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 46.25 KB (47361) | 46.25 KB (47361) | + | Line Count | 1861 | 1861 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_gc_content_plot-2_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 54.15 KB (55448) | 54.15 KB (55448) | + | Line Count | 2159 | 2159 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_gc_content_plot-2_Percentages.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 53.86 KB (55153) | 53.86 KB (55153) | + | Line Count | 2177 | 2177 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_gc_content_plot_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 54.13 KB (55433) | 54.13 KB (55433) | + | Line Count | 2159 | 2159 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_gc_content_plot_Percentages.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 53.87 KB (55159) | 53.87 KB (55159) | + | Line Count | 2177 | 2177 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_quality_scores_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 43.01 KB (44039) | 43.01 KB (44039) | + | Line Count | 1638 | 1638 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_per_sequence_quality_scores_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 43.15 KB (44183) | 43.15 KB (44183) | + | Line Count | 1644 | 1644 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_counts_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 35.45 KB (36305) | 35.45 KB (36305) | + | Line Count | 1422 | 1422 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_counts_plot-2_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 35.81 KB (36666) | 35.81 KB (36666) | + | Line Count | 1460 | 1460 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_counts_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 35.40 KB (36252) | 35.40 KB (36252) | + | Line Count | 1422 | 1422 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_counts_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 35.81 KB (36666) | 35.81 KB (36666) | + | Line Count | 1460 | 1460 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_duplication_levels_plot-2_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 44.95 KB (46031) | 44.95 KB (46031) | + | Line Count | 1767 | 1767 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_duplication_levels_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 44.95 KB (46030) | 44.95 KB (46030) | + | Line Count | 1767 | 1767 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_fastqc_sequence_length_distribution_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 48.56 KB (49725) | 48.56 KB (49725) | + | Line Count | 1893 | 1893 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_featurecounts_biotype_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 33.74 KB (34546) | 33.74 KB (34546) | + | Line Count | 1412 | 1412 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_featurecounts_biotype_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.79 KB (35620) | 34.79 KB (35620) | + | Line Count | 1470 | 1470 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_picard_deduplication_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.81 KB (35643) | 34.81 KB (35643) | + | Line Count | 1355 | 1355 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_picard_deduplication_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.90 KB (35733) | 34.90 KB (35733) | + | Line Count | 1413 | 1413 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_preseq_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 41.21 KB (42202) | 41.21 KB (42202) | + | Line Count | 1559 | 1559 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_qualimap_gene_coverage_profile_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 48.16 KB (49316) | 48.16 KB (49316) | + | Line Count | 1938 | 1938 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_qualimap_gene_coverage_profile_Normalised.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 49.28 KB (50467) | 49.28 KB (50467) | + | Line Count | 1970 | 1970 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_qualimap_genomic_origin_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.28 KB (35107) | 34.28 KB (35107) | + | Line Count | 1399 | 1399 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_qualimap_genomic_origin_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.38 KB (35206) | 34.38 KB (35206) | + | Line Count | 1457 | 1457 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_infer_experiment_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 30.49 KB (31218) | 30.49 KB (31218) | + | Line Count | 1296 | 1296 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_inner_distance_plot_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 33.07 KB (33862) | 33.07 KB (33862) | + | Line Count | 1348 | 1348 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_inner_distance_plot_Percentages.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 31.56 KB (32322) | 31.56 KB (32322) | + | Line Count | 1318 | 1318 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_annotation_junctions_plot_Events.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 31.10 KB (31849) | 31.10 KB (31849) | + | Line Count | 1269 | 1269 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_annotation_junctions_plot_Events_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 30.61 KB (31345) | 30.61 KB (31345) | + | Line Count | 1254 | 1254 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_annotation_junctions_plot_Junctions.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 32.11 KB (32877) | 32.11 KB (32877) | + | Line Count | 1301 | 1301 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_annotation_junctions_plot_Junctions_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 30.99 KB (31731) | 30.99 KB (31731) | + | Line Count | 1262 | 1262 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_saturation_plot_All_Junctions.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.14 KB (34959)  | 34.14 KB (34961)  | + | Line Count | 1368 | 1368 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_saturation_plot_Known_Junctions.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.16 KB (34975)  | 34.15 KB (34972)  | + | Line Count | 1382 | 1382 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_junction_saturation_plot_Novel_Junctions.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 34.14 KB (34956) | 34.14 KB (34956) | + | Line Count | 1368 | 1368 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_read_distribution_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 33.84 KB (34650) | 33.84 KB (34650) | + | Line Count | 1399 | 1399 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_read_distribution_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 32.90 KB (33686) | 32.90 KB (33686) | + | Line Count | 1401 | 1401 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_rseqc_read_dups_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 43.24 KB (44282) | 43.24 KB (44282) | + | Line Count | 1720 | 1720 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_salmon_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 58.50 KB (59907)  | 58.24 KB (59634)  | + | Line Count | 2346  | 2336  | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_samtools-idxstats-mapped-reads-plot_Normalised_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 31.71 KB (32474) | 31.71 KB (32474) | + | Line Count | 1281 | 1281 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 33.74 KB (34550) | 33.74 KB (34550) | + | Line Count | 1346 | 1346 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_samtools-idxstats-mapped-reads-plot_Raw_Counts.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 31.85 KB (32611) | 31.85 KB (32611) | + | Line Count | 1260 | 1260 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_samtools_alignment_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 28.25 KB (28928) | 28.25 KB (28928) | + | Line Count | 1152 | 1152 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_samtools_alignment_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 28.35 KB (29030) | 28.35 KB (29030) | + | Line Count | 1210 | 1210 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_star_alignment_plot_1.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 38.72 KB (39645) | 38.72 KB (39645) | + | Line Count | 1549 | 1549 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_plots/svg/mqc_star_alignment_plot_1_pc.svg + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 39.07 KB (40004) | 39.07 KB (40004) | + | Line Count | 1587 | 1587 | + '--------------------------------------------------------------------' + + - multiqc/star_salmon/multiqc_report.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.47 MB (1540021)  | 1.47 MB (1539898)  | + | Line Count | 9656 | 9656 | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 549.00 B (549)  | 561.00 B (561)  | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.79 KB (1828)  | 1.79 KB (1829)  | + | Line Count | 49 | 49 | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.42 KB (11698)  | 11.46 KB (11733)  | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.74 KB (3832) | 3.74 KB (3832) | + | Line Count | 46 | 46 | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.62 KB (3707)  | 3.67 KB (3754)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/RAP1_IAA_30M_REP1/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.76 KB (4871) | 4.76 KB (4871) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 306.00 B (306)  | 316.00 B (316)  | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.78 KB (1827) | 1.78 KB (1827) | + | Line Count | 49 | 49 | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.97 KB (4070) | 3.97 KB (4070) | + | Line Count | 51 | 51 | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 322.00 B (322)  | 315.00 B (315)  | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.78 KB (1827) | 1.78 KB (1827) | + | Line Count | 49 | 49 | + '--------------------------------------------------------------------' + + - salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.97 KB (4070) | 3.97 KB (4070) | + | Line Count | 51 | 51 | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 548.00 B (548)  | 561.00 B (561)  | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.79 KB (1828)  | 1.79 KB (1829)  | + | Line Count | 49 | 49 | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.46 KB (11730)  | 11.47 KB (11746)  | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.74 KB (3833) | 3.74 KB (3833) | + | Line Count | 46 | 46 | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.65 KB (3741)  | 3.66 KB (3751)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/WT_REP1/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.74 KB (4852) | 4.74 KB (4852) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 556.00 B (556)  | 572.00 B (572)  | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.79 KB (1828) | 1.79 KB (1828) | + | Line Count | 49 | 49 | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.46 KB (11733)  | 11.46 KB (11734)  | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.74 KB (3832) | 3.74 KB (3832) | + | Line Count | 46 | 46 | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.62 KB (3706)  | 3.63 KB (3712)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/WT_REP2/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.72 KB (4830) | 4.72 KB (4830) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/deseq2.dds.RData + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.44 KB (7617)  | 7.43 KB (7604)  | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/deseq2.pca.vals.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 319.00 B (319)  | 321.00 B (321)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/deseq2.plots.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.19 KB (9415)  | 9.20 KB (9424)  | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/deseq2.sample.dists.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 509.00 B (509)  | 507.00 B (507)  | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.00 B (10) | 10.00 B (10) | + | Line Count | 1 | 1 | + '--------------------------------------------------------------------' + + - salmon/deseq2_qc/size_factors/deseq2.size_factors.RData + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 191.00 B (191) | 191.00 B (191) | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_counts.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.37 KB (6519)  | 6.36 KB (6516)  | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_counts_length_scaled.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.67 KB (8874)  | 8.67 KB (8877)  | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_counts_length_scaled.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.65 KB (9881)  | 9.66 KB (9894)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_counts_scaled.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.64 KB (8848)  | 8.64 KB (8852)  | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_counts_scaled.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.46 KB (9686)  | 9.57 KB (9798)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.gene_tpm.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.24 KB (7416)  | 7.26 KB (7431)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.transcript_counts.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.39 KB (6539)  | 6.38 KB (6533)  | + '--------------------------------------------------------------------' + + - salmon/salmon.merged.transcript_tpm.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.46 KB (7636)  | 7.47 KB (7651)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.60 MB (3778318)  | 3.60 MB (3778293)  | + | Total Reads | 94912 | 94912 | + | # Mapped | 94912 (100.00%) | 94912 (100.00%) | + | # Duplicate | 11688 (12.31%) | 11688 (12.31%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.89 KB (1936) | 1.89 KB (1936) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 561.00 B (561)  | 565.00 B (565)  | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.24 KB (1267)  | 1.24 KB (1268)  | + | Line Count | 48 | 48 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.46 KB (11732) | 11.46 KB (11732) | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.73 KB (2795) | 2.73 KB (2795) | + | Line Count | 39 | 39 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.65 KB (3734)  | 3.66 KB (3747)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_IAA_30M_REP1/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.75 KB (4866) | 4.75 KB (4866) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.62 MB (1703202)  | 1.62 MB (1703065)  | + | Total Reads | 49040 | 49040 | + | # Mapped | 49040 (100.00%) | 49040 (100.00%) | + | # Duplicate | 36290 (74.00%) | 36290 (74.00%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.32 KB (1352) | 1.32 KB (1352) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 313.00 B (313)  | 304.00 B (304)  | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.24 KB (1266) | 1.24 KB (1266) | + | Line Count | 48 | 48 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.73 KB (2794) | 2.73 KB (2794) | + | Line Count | 39 | 39 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.29 KB (3374) | 3.29 KB (3374) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.72 KB (4831) | 4.72 KB (4831) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.13 MB (3279083)  | 3.13 MB (3279085)  | + | Total Reads | 98338 | 98338 | + | # Mapped | 98338 (100.00%) | 98338 (100.00%) | + | # Duplicate | 78936 (80.27%) | 78936 (80.27%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.03 KB (2080) | 2.03 KB (2080) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 317.00 B (317)  | 325.00 B (325)  | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.24 KB (1267) | 1.24 KB (1267) | + | Line Count | 48 | 48 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.73 KB (2796) | 2.73 KB (2796) | + | Line Count | 39 | 39 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.39 KB (3468)  | 3.39 KB (3467)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.76 KB (4879) | 4.76 KB (4879) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.86 MB (7196616)  | 6.86 MB (7196472)  | + | Total Reads | 188243 | 188243 | + | # Mapped | 188243 (100.00%) | 188243 (100.00%) | + | # Duplicate | 38470 (20.44%) | 38470 (20.44%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1.markdup.sorted.bam.bai + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.45 KB (3536) | 3.45 KB (3536) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 585.00 B (585)  | 577.00 B (577)  | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.24 KB (1268)  | 1.24 KB (1267)  | + | Line Count | 48 | 48 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.46 KB (11733)  | 11.46 KB (11739)  | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.73 KB (2795) | 2.73 KB (2795) | + | Line Count | 39 | 39 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.65 KB (3737)  | 3.64 KB (3727)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.73 KB (4848) | 4.73 KB (4848) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.41 MB (3570486)  | 3.41 MB (3570488)  | + | Total Reads | 94419 | 94419 | + | # Mapped | 94419 (100.00%) | 94419 (100.00%) | + | # Duplicate | 12165 (12.88%) | 12165 (12.88%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2.markdup.sorted.bam.bai + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.84 KB (1880) | 1.84 KB (1880) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/aux_info/fld.gz + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 579.00 B (579)  | 585.00 B (585)  | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/aux_info/meta_info.json + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.24 KB (1267)  | 1.24 KB (1266)  | + | Line Count | 48 | 48 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/libParams/flenDist.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.46 KB (11732)  | 11.46 KB (11734)  | + | Line Count | 2 | 2 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/logs/salmon_quant.log + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.73 KB (2794) | 2.73 KB (2794) | + | Line Count | 39 | 39 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/quant.genes.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.61 KB (3698)  | 3.61 KB (3697)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2/quant.sf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.71 KB (4824) | 4.71 KB (4824) | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/deseq2_qc/deseq2.plots.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.17 KB (9386) | 9.17 KB (9386) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.71 KB (5849) | 5.71 KB (5849) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.34 KB (6497) | 6.34 KB (6497) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.47 KB (6624) | 6.47 KB (6624) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.84 KB (5976) | 5.84 KB (5976) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.76 KB (5896) | 5.76 KB (5896) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.90 KB (5022) | 4.90 KB (5022) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.82 KB (4940) | 4.82 KB (4940) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.88 KB (4997) | 4.88 KB (4997) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.94 KB (5061) | 4.94 KB (5061) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.94 KB (5057) | 4.94 KB (5057) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.02 KB (10265) | 10.02 KB (10265) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.32 KB (10572) | 10.32 KB (10572) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.96 KB (11223) | 10.96 KB (11223) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.15 KB (10395) | 10.15 KB (10395) | + '--------------------------------------------------------------------' + + - star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.67 KB (9901) | 9.67 KB (9901) | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.94 KB (1988) | 1.94 KB (1988) | + | Line Count | 37 | 37 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_IAA_30M_REP1.Log.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.99 KB (9209) | 8.99 KB (9209) | + | Line Count | 179 | 179 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.94 KB (1984) | 1.94 KB (1984) | + | Line Count | 37 | 37 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP1.Log.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.27 KB (8466) | 8.27 KB (8466) | + | Line Count | 159 | 159 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 447.00 B (447) | 447.00 B (447) | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.94 KB (1986) | 1.94 KB (1986) | + | Line Count | 37 | 37 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP2.Log.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.27 KB (8466) | 8.27 KB (8466) | + | Line Count | 159 | 159 | + '--------------------------------------------------------------------' + + - star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 447.00 B (447) | 447.00 B (447) | + | Line Count | 6 | 6 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP1.Log.final.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.95 KB (1992) | 1.95 KB (1992) | + | Line Count | 37 | 37 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP1.Log.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.62 KB (8830) | 8.62 KB (8830) | + | Line Count | 179 | 179 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP1.Log.progress.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 565.00 B (565) | 565.00 B (565) | + | Line Count | 7 | 7 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP2.Log.final.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.94 KB (1988) | 1.94 KB (1988) | + | Line Count | 37 | 37 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP2.Log.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.62 KB (8829) | 8.62 KB (8829) | + | Line Count | 179 | 179 | + '--------------------------------------------------------------------' + + - star_salmon/log/WT_REP2.Log.progress.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 565.00 B (565) | 565.00 B (565) | + | Line Count | 7 | 7 | + '--------------------------------------------------------------------' + + - star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.26 KB (3342) | 3.26 KB (3342) | + | Line Count | 112 | 112 | + '--------------------------------------------------------------------' + + - star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.42 KB (1452) | 1.42 KB (1452) | + | Line Count | 10 | 10 | + '--------------------------------------------------------------------' + + - star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.42 KB (1451) | 1.42 KB (1451) | + | Line Count | 10 | 10 | + '--------------------------------------------------------------------' + + - star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.25 KB (3331) | 3.25 KB (3331) | + | Line Count | 112 | 112 | + '--------------------------------------------------------------------' + + - star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.22 KB (3300) | 3.22 KB (3300) | + | Line Count | 112 | 112 | + '--------------------------------------------------------------------' + + - star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.28 KB (11553) | 11.28 KB (11553) | + | Line Count | 320 | 320 | + '--------------------------------------------------------------------' + + - star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.05 KB (11315) | 11.05 KB (11315) | + | Line Count | 316 | 316 | + '--------------------------------------------------------------------' + + - star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.05 KB (11316) | 11.05 KB (11316) | + | Line Count | 316 | 316 | + '--------------------------------------------------------------------' + + - star_salmon/qualimap/WT_REP1/qualimapReport.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.27 KB (11544) | 11.27 KB (11544) | + | Line Count | 320 | 320 | + '--------------------------------------------------------------------' + + - star_salmon/qualimap/WT_REP2/qualimapReport.html + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 11.27 KB (11543) | 11.27 KB (11543) | + | Line Count | 320 | 320 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.38 KB (8586) | 8.38 KB (8586) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.41 KB (8616) | 8.41 KB (8616) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.41 KB (8613) | 8.41 KB (8613) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.77 MB (1851943)  | 1.77 MB (1851942)  | + | Line Count | 38992 | 38992 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.16 MB (3313008) | 3.16 MB (3313008) | + | Line Count | 69249 | 69249 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.74 MB (1821557) | 1.74 MB (1821557) | + | Line Count | 38290 | 38290 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.57 KB (12875) | 12.57 KB (12875) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.57 KB (12873) | 12.57 KB (12873) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.67 KB (12974) | 12.67 KB (12974) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.63 KB (12929) | 12.63 KB (12929) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.68 KB (12986) | 12.68 KB (12986) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.65 KB (12953) | 12.65 KB (12953) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.59 KB (12897) | 12.59 KB (12897) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.69 KB (12993) | 12.69 KB (12993) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.61 KB (12913) | 12.61 KB (12913) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.69 KB (12997) | 12.69 KB (12997) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.30 KB (5427)  | 5.30 KB (5430)  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.27 KB (5397)  | 5.27 KB (5398)  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.28 KB (5410) | 5.28 KB (5410) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.31 KB (5441)  | 5.31 KB (5436)  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 5.29 KB (5419)  | 5.30 KB (5424)  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 638.00 B (638)  | 640.00 B (640)  | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 637.00 B (637) | 637.00 B (637) | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 639.00 B (639) | 639.00 B (639) | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 652.00 B (652)  | 651.00 B (651)  | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 634.00 B (634) | 634.00 B (634) | + | Line Count | 12 | 12 | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.61 KB (6765) | 6.61 KB (6765) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.43 KB (6586) | 6.43 KB (6586) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.59 KB (7773) | 7.59 KB (7773) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.20 KB (8397) | 8.20 KB (8397) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.77 KB (6928) | 6.77 KB (6928) | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.34 KB (6493)  | 6.35 KB (6500)  | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.64 KB (3730)  | 3.64 KB (3728)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts_length_scaled.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.67 KB (8877)  | 8.66 KB (8866)  | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts_length_scaled.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.65 KB (9877)  | 9.65 KB (9885)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts_scaled.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 8.64 KB (8847)  | 8.64 KB (8852)  | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_counts_scaled.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.63 KB (9861)  | 9.61 KB (9839)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.gene_tpm.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.24 KB (7417)  | 7.24 KB (7415)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.transcript_counts.rds + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.35 KB (6504)  | 6.36 KB (6513)  | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.transcript_counts.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.86 KB (3950)  | 3.86 KB (3948)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - star_salmon/salmon.merged.transcript_tpm.tsv + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 7.46 KB (7637)  | 7.46 KB (7635)  | + | Line Count | 126 | 126 | + '--------------------------------------------------------------------' + + - trimgalore/RAP1_IAA_30M_REP1_1.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.65 KB (2711) | 2.65 KB (2711) | + | Line Count | 115 | 115 | + '--------------------------------------------------------------------' + + - trimgalore/RAP1_IAA_30M_REP1_2.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.86 KB (2928) | 2.86 KB (2928) | + | Line Count | 120 | 120 | + '--------------------------------------------------------------------' + + - trimgalore/RAP1_UNINDUCED_REP1.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.77 KB (2841) | 2.77 KB (2841) | + | Line Count | 119 | 119 | + '--------------------------------------------------------------------' + + - trimgalore/RAP1_UNINDUCED_REP2.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.79 KB (2855)  | 2.79 KB (2856)  | + | Line Count | 117 | 117 | + '--------------------------------------------------------------------' + + - trimgalore/WT_REP1_1.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.72 KB (2784)  | 2.72 KB (2785)  | + | Line Count | 118 | 118 | + '--------------------------------------------------------------------' + + - trimgalore/WT_REP1_2.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.90 KB (2969)  | 2.90 KB (2970)  | + | Line Count | 121 | 121 | + '--------------------------------------------------------------------' + + - trimgalore/WT_REP2_1.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.66 KB (2724)  | 2.66 KB (2723)  | + | Line Count | 117 | 117 | + '--------------------------------------------------------------------' + + - trimgalore/WT_REP2_2.fastq.gz_trimming_report.txt + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 2.84 KB (2907)  | 2.84 KB (2906)  | + | Line Count | 119 | 119 | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/RAP1_IAA_30M_REP1_1_val_1_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 357.75 KB (366339) | 357.75 KB (366339) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/RAP1_IAA_30M_REP1_2_val_2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 345.86 KB (354156) | 345.86 KB (354156) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/RAP1_UNINDUCED_REP1_trimmed_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 359.13 KB (367744) | 359.13 KB (367744) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/RAP1_UNINDUCED_REP2_trimmed_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 359.31 KB (367929) | 359.31 KB (367929) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/WT_REP1_1_val_1_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 358.76 KB (367375) | 358.76 KB (367375) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/WT_REP1_2_val_2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 350.91 KB (359332) | 350.91 KB (359332) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/WT_REP2_1_val_1_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 357.13 KB (365705) | 357.13 KB (365705) | + '--------------------------------------------------------------------' + + - trimgalore/fastqc/WT_REP2_2_val_2_fastqc.zip + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 353.42 KB (361903) | 353.42 KB (361903) | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 1/864 files) + + - star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 565.00 B (565)  | 447.00 B (447)  | + | Line Count | 7  | 6  | + '--------------------------------------------------------------------' + +=== Level0 (Not Found, Crate1: 8 files, Crate2: 8 files) + + - Only in Crate1: + + - outputs/multiqc/star_salmon/multiqc_data/mqc_mqc_mplplot_gtnuqiebfc_1.txt + - outputs/multiqc/star_salmon/multiqc_plots/pdf/mqc_mqc_mplplot_gtnuqiebfc_1.pdf + - outputs/multiqc/star_salmon/multiqc_plots/png/mqc_mqc_mplplot_gtnuqiebfc_1.png + - outputs/multiqc/star_salmon/multiqc_plots/svg/mqc_mqc_mplplot_gtnuqiebfc_1.svg + - outputs/pipeline_info/execution_report_2022-09-08_06-28-19.html + - outputs/pipeline_info/execution_timeline_2022-09-08_06-28-19.html + - outputs/pipeline_info/execution_trace_2022-09-08_06-28-19.txt + - outputs/pipeline_info/pipeline_dag_2022-09-08_06-28-19.dot + + - Only in Crate2: + + - outputs/multiqc/star_salmon/multiqc_data/mqc_mqc_mplplot_vpgladqwtb_1.txt + - outputs/multiqc/star_salmon/multiqc_plots/pdf/mqc_mqc_mplplot_vpgladqwtb_1.pdf + - outputs/multiqc/star_salmon/multiqc_plots/png/mqc_mqc_mplplot_vpgladqwtb_1.png + - outputs/multiqc/star_salmon/multiqc_plots/svg/mqc_mqc_mplplot_vpgladqwtb_1.svg + - outputs/pipeline_info/execution_report_2022-09-08_06-08-08.html + - outputs/pipeline_info/execution_timeline_2022-09-08_06-08-08.html + - outputs/pipeline_info/execution_trace_2022-09-08_06-08-08.txt + - outputs/pipeline_info/pipeline_dag_2022-09-08_06-08-08.dot + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 557 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 306 files | + | Unacceptable Differences | ⭐ | Different Features | 1 files | + | Not Reproduced | | Not Found | 16 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/rnaseq_diff_env.log b/tests/comparison_results/rnaseq_diff_env.log new file mode 100644 index 0000000..f162c18 --- /dev/null +++ b/tests/comparison_results/rnaseq_diff_env.log @@ -0,0 +1,89 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/rnaseq_1st.json + Crate2: ./tests/example_crate/rnaseq_mac.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | nf-core - rnaseq  | nf-core - rnaseq - v3.7  | +| WF ID | 20da6ea5-de91-4973-ac20-216882357a0d | 20da6ea5-de91-4973-ac20-216882357a0d | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Nextflow | Nextflow | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | nextflow | nextflow | +| WF Eng Version | 22.04.4 | 22.04.4 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE  | EXECUTOR_ERROR  | +| ExitCode | 0  | 1  | +| Start Time | 2022-09-08 06:28:11 | 2022-09-14 08:42:09 | +| End Time | 2022-09-08 06:45:53 | 2022-09-14 08:44:23 | +| Duration | 17m 42s | 2m 14s | +| # Attachments | 147 files | 147 files | +| # Intermediate | 3342 files  | 36 files  | +| # Outputs | 872 files (25 EDAM-assigned files)  | 4 files (0 EDAM-assigned files)  | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 0/0 files) + +=== Level2 ⭐⭐ (Similar Features, 0/0 files) + +=== Level1 ⭐ (Different Features, 0/0 files) + +=== Level0 (Not Found, Crate1: 25 files, Crate2: 0 files) + + - Only in Crate1: + + - outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam + - outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam + - outputs/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam + - outputs/star_salmon/WT_REP1.markdup.sorted.bam + - outputs/star_salmon/WT_REP2.markdup.sorted.bam + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed + - outputs/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf + - outputs/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf + - outputs/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf + - outputs/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf + - outputs/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf + - outputs/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf + - outputs/star_salmon/stringtie/WT_REP1.coverage.gtf + - outputs/star_salmon/stringtie/WT_REP1.transcripts.gtf + - outputs/star_salmon/stringtie/WT_REP2.coverage.gtf + - outputs/star_salmon/stringtie/WT_REP2.transcripts.gtf + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 0 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 0 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 25 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/rnaseq_diff_ver.log b/tests/comparison_results/rnaseq_diff_ver.log new file mode 100644 index 0000000..3475e69 --- /dev/null +++ b/tests/comparison_results/rnaseq_diff_ver.log @@ -0,0 +1,181 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/rnaseq_1st.json + Crate2: ./tests/example_crate/rnaseq_v3.6.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | nf-core - rnaseq  | nf-core - rnaseq - v3.6  | +| WF ID | 20da6ea5-de91-4973-ac20-216882357a0d | fbb91c56-fbbb-4d09-86f6-c44cba7d8bcc | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Nextflow | Nextflow | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | nextflow | nextflow | +| WF Eng Version | 22.04.4 | 22.04.4 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-08 06:28:11 | 2022-09-14 14:30:26 | +| End Time | 2022-09-08 06:45:53 | 2022-09-14 14:49:28 | +| Duration | 17m 42s | 19m 2s | +| # Attachments | 147 files  | 182 files  | +| # Intermediate | 3342 files  | 3340 files  | +| # Outputs | 872 files (25 EDAM-assigned files) | 872 files (25 EDAM-assigned files) | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 13/25 files) + + - star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed + - star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf + - star_salmon/stringtie/WT_REP1.coverage.gtf + - star_salmon/stringtie/WT_REP2.coverage.gtf + +=== Level2 ⭐⭐ (Similar Features, 12/25 files) + + - star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.60 MB (3778318)  | 3.60 MB (3778271)  | + | Total Reads | 94912 | 94912 | + | # Mapped | 94912 (100.00%) | 94912 (100.00%) | + | # Duplicate | 11688 (12.31%) | 11688 (12.31%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.62 MB (1703202)  | 1.62 MB (1703219)  | + | Total Reads | 49040 | 49040 | + | # Mapped | 49040 (100.00%) | 49040 (100.00%) | + | # Duplicate | 36290 (74.00%) | 36290 (74.00%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.13 MB (3279083)  | 3.13 MB (3279025)  | + | Total Reads | 98338 | 98338 | + | # Mapped | 98338 (100.00%) | 98338 (100.00%) | + | # Duplicate | 78936 (80.27%) | 78936 (80.27%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.86 MB (7196616)  | 6.86 MB (7192272)  | + | Total Reads | 188243  | 188241  | + | # Mapped | 188243 (100.00%)  | 188241 (100.00%)  | + | # Duplicate | 38470 (20.44%) | 38470 (20.44%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.41 MB (3570486)  | 3.41 MB (3570473)  | + | Total Reads | 94419 | 94419 | + | # Mapped | 94419 (100.00%) | 94419 (100.00%) | + | # Duplicate | 12165 (12.88%) | 12165 (12.88%) | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 22.46 KB (22995)  | 22.32 KB (22856)  | + | Line Count | 162  | 161  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.96 KB (11225)  | 10.89 KB (11156)  | + | Line Count | 161  | 160  | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 38.07 KB (38980) | 38.07 KB (38980) | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 37.96 KB (38869) | 37.96 KB (38869) | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 38.14 KB (39058) | 38.14 KB (39058) | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/WT_REP1.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 37.97 KB (38879) | 37.97 KB (38879) | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/WT_REP2.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 37.82 KB (38729) | 37.82 KB (38729) | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 0/25 files) + +=== Level0 (Not Found, Crate1: 0 files, Crate2: 0 files) + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 13 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 12 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 0 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/rnaseq_missing_data.log b/tests/comparison_results/rnaseq_missing_data.log new file mode 100644 index 0000000..93c36d4 --- /dev/null +++ b/tests/comparison_results/rnaseq_missing_data.log @@ -0,0 +1,182 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/rnaseq_1st.json + Crate2: ./tests/example_crate/rnaseq_small.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | nf-core - rnaseq  | nf-core - ... with Small Test Data | +| WF ID | 20da6ea5-de91-4973-ac20-216882357a0d | 20da6ea5-de91-4973-ac20-216882357a0d | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Nextflow | Nextflow | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | nextflow | nextflow | +| WF Eng Version | 22.04.4 | 22.04.4 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-08 06:28:11 | 2022-09-15 09:07:41 | +| End Time | 2022-09-08 06:45:53 | 2022-09-15 09:22:17 | +| Duration | 17m 42s | 14m 36s | +| # Attachments | 147 files | 147 files | +| # Intermediate | 3342 files  | 2760 files  | +| # Outputs | 872 files (25 EDAM-assigned files)  | 747 files (20 EDAM-assigned files)  | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 8/20 files) + + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf + - star_salmon/stringtie/WT_REP2.coverage.gtf + - star_salmon/stringtie/WT_REP2.transcripts.gtf + +=== Level2 ⭐⭐ (Similar Features, 5/20 files) + + - star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.62 MB (1703202)  | 1.62 MB (1703131)  | + | Total Reads | 49040 | 49040 | + | # Mapped | 49040 (100.00%) | 49040 (100.00%) | + | # Duplicate | 36290 (74.00%) | 36290 (74.00%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.41 MB (3570486)  | 3.41 MB (3570482)  | + | Total Reads | 94419 | 94419 | + | # Mapped | 94419 (100.00%) | 94419 (100.00%) | + | # Duplicate | 12165 (12.88%) | 12165 (12.88%) | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 38.14 KB (39058)  | 38.00 KB (38913)  | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/WT_REP1.coverage.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 14.12 KB (14460)  | 13.75 KB (14077)  | + | Line Count | 156  | 152  | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/WT_REP1.transcripts.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 37.97 KB (38879)  | 37.91 KB (38815)  | + | Line Count | 259 | 259 | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 7/20 files) + + - star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.13 MB (3279083)  | 1.68 MB (1758332)  | + | Total Reads | 98338  | 49223  | + | # Mapped | 98338 (100.00%)  | 49223 (100.00%)  | + | # Duplicate | 78936 (80.27%)  | 36278 (73.70%)  | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.86 MB (7196616)  | 3.48 MB (3648457)  | + | Total Reads | 188243  | 92675  | + | # Mapped | 188243 (100.00%)  | 92675 (100.00%)  | + | # Duplicate | 38470 (20.44%)  | 13592 (14.67%)  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 9.99 KB (10233)  | 7.10 KB (7269)  | + | Line Count | 72  | 51  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 4.82 KB (4933)  | 3.40 KB (3484)  | + | Line Count | 71  | 50  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 22.46 KB (22995)  | 13.94 KB (14270)  | + | Line Count | 162  | 101  | + '--------------------------------------------------------------------' + + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 10.96 KB (11225)  | 6.78 KB (6946)  | + | Line Count | 161  | 100  | + '--------------------------------------------------------------------' + + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 12.62 KB (12918)  | 10.69 KB (10948)  | + | Line Count | 139  | 118  | + '--------------------------------------------------------------------' + +=== Level0 (Not Found, Crate1: 5 files, Crate2: 0 files) + + - Only in Crate1: + + - outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed + - outputs/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed + - outputs/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf + - outputs/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 8 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 5 files | + | Unacceptable Differences | ⭐ | Different Features | 7 files | + | Not Reproduced | | Not Found | 5 files | + '---------------------------------------------------------------------------' + diff --git a/tests/comparison_results/rnaseq_same_env.log b/tests/comparison_results/rnaseq_same_env.log new file mode 100644 index 0000000..1105c8d --- /dev/null +++ b/tests/comparison_results/rnaseq_same_env.log @@ -0,0 +1,132 @@ +Tonkaz 0.2.2 + +Checking Crate2 based on Crate1: + + Crate1: ./tests/example_crate/rnaseq_1st.json + Crate2: ./tests/example_crate/rnaseq_2nd.json + +.----------------------------------------------------------------------------------------------. +| | Crate1 | Crate2 | +|----------------|--------------------------------------|--------------------------------------| +| WF Name | nf-core - rnaseq | nf-core - rnaseq | +| WF ID | 20da6ea5-de91-4973-ac20-216882357a0d | 20da6ea5-de91-4973-ac20-216882357a0d | +| WF Ver | 1.0.0 | 1.0.0 | +| WF Type | Nextflow | Nextflow | +| WF Type Ver | 1.0 | 1.0 | +| WF Eng Name | nextflow | nextflow | +| WF Eng Version | 22.04.4 | 22.04.4 | +| Sapporo Ver | 1.4.8 | 1.4.8 | +| Run Name | example_test | example_test | +| Run State | COMPLETE | COMPLETE | +| ExitCode | 0 | 0 | +| Start Time | 2022-09-08 06:28:11 | 2022-09-08 06:08:01 | +| End Time | 2022-09-08 06:45:53 | 2022-09-08 06:25:56 | +| Duration | 17m 42s | 17m 55s | +| # Attachments | 147 files | 147 files | +| # Intermediate | 3342 files | 3342 files | +| # Outputs | 872 files (25 EDAM-assigned files) | 872 files (25 EDAM-assigned files) | +'----------------------------------------------------------------------------------------------' + * EDAM extensions: .bam/.bb/.bed/.bw/.fa/.fasta/.fastq/.fastq.gz/.fq/.fq.gz/.gtf/.gff/.sam/.vcf/.vcf.gz/.wig + +Comparing workflow results... +Calculate the reproducibility level by comparing the EDAM-assigned output files of Crate1 and Crate2. (option `--all` to use all output files) + +Reproducibility level is defined as follows: + + - Level3 ⭐⭐⭐ : Files are identical with the same checksum + - Level2 ⭐⭐ : Files are different, but their features (file size, map rate, etc.) are similar (within threshold: 0.05) + - Level1 ⭐ : Files are different, and their features are different (beyond threshold) + - Level0 : File not found + + Level3: "Fully Reproduced" <---> Level0: "Not Reproduced" + +=== Level3 ⭐⭐⭐ (Same Checksum, 20/25 files) + + - star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed + - star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed + - star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf + - star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf + - star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf + - star_salmon/stringtie/WT_REP1.coverage.gtf + - star_salmon/stringtie/WT_REP1.transcripts.gtf + - star_salmon/stringtie/WT_REP2.coverage.gtf + - star_salmon/stringtie/WT_REP2.transcripts.gtf + +=== Level2 ⭐⭐ (Similar Features, 5/25 files) + + - star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.60 MB (3778318)  | 3.60 MB (3778293)  | + | Total Reads | 94912 | 94912 | + | # Mapped | 94912 (100.00%) | 94912 (100.00%) | + | # Duplicate | 11688 (12.31%) | 11688 (12.31%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 1.62 MB (1703202)  | 1.62 MB (1703065)  | + | Total Reads | 49040 | 49040 | + | # Mapped | 49040 (100.00%) | 49040 (100.00%) | + | # Duplicate | 36290 (74.00%) | 36290 (74.00%) | + '--------------------------------------------------------------------' + + - star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.13 MB (3279083)  | 3.13 MB (3279085)  | + | Total Reads | 98338 | 98338 | + | # Mapped | 98338 (100.00%) | 98338 (100.00%) | + | # Duplicate | 78936 (80.27%) | 78936 (80.27%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP1.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 6.86 MB (7196616)  | 6.86 MB (7196472)  | + | Total Reads | 188243 | 188243 | + | # Mapped | 188243 (100.00%) | 188243 (100.00%) | + | # Duplicate | 38470 (20.44%) | 38470 (20.44%) | + '--------------------------------------------------------------------' + + - star_salmon/WT_REP2.markdup.sorted.bam + .--------------------------------------------------------------------. + | | in Crate1 | in Crate2 | + |----------------|-------------------------|-------------------------| + | File Size | 3.41 MB (3570486)  | 3.41 MB (3570488)  | + | Total Reads | 94419 | 94419 | + | # Mapped | 94419 (100.00%) | 94419 (100.00%) | + | # Duplicate | 12165 (12.88%) | 12165 (12.88%) | + '--------------------------------------------------------------------' + +=== Level1 ⭐ (Different Features, 0/25 files) + +=== Level0 (Not Found, Crate1: 0 files, Crate2: 0 files) + +Summarize compare result: + + .---------------------------------------------------------------------------. + | Reproducibility | Level | Definition | File # | + |---------------------------|-----------|---------------------|-------------| + | Fully Reproduced | ⭐⭐⭐ | Same Checksum | 20 files | + | Acceptable Differences | ⭐⭐ | Similar Features | 5 files | + | Unacceptable Differences | ⭐ | Different Features | 0 files | + | Not Reproduced | | Not Found | 0 files | + '---------------------------------------------------------------------------' + diff --git a/tests/dump_all_comparison_results.sh b/tests/dump_all_comparison_results.sh new file mode 100644 index 0000000..7bd65f3 --- /dev/null +++ b/tests/dump_all_comparison_results.sh @@ -0,0 +1,18 @@ +#!/usr/bin/env bash +set -euxo pipefail + +HERE=$( + cd $(dirname $0) + pwd +) +cd $HERE/.. + +mv ./tests/comparison_results/rnaseq_same_env.json ./tests/comparison_results/rnaseq_same_env.log +mv ./tests/comparison_results/rnaseq_diff_env.json ./tests/comparison_results/rnaseq_diff_env.log +mv ./tests/comparison_results/rnaseq_diff_ver.json ./tests/comparison_results/rnaseq_diff_ver.log +mv ./tests/comparison_results/rnaseq_missing_data.json ./tests/comparison_results/rnaseq_missing_data.log +mv ./tests/comparison_results/rnaseq_all_files.json ./tests/comparison_results/rnaseq_all_files.log +mv ./tests/comparison_results/jga_same_env.json ./tests/comparison_results/jga_same_env.log +mv ./tests/comparison_results/jga_diff_env.json ./tests/comparison_results/jga_diff_env.log +mv ./tests/comparison_results/gatk_same_env.json ./tests/comparison_results/gatk_same_env.log +mv ./tests/comparison_results/gatk_diff_env.json ./tests/comparison_results/gatk_diff_env.log diff --git a/tests/rnaseq_all_files_test.ts b/tests/rnaseq_all_files_test.ts new file mode 100644 index 0000000..c5e1139 --- /dev/null +++ b/tests/rnaseq_all_files_test.ts @@ -0,0 +1,15 @@ +import { args, compare, crate } from "../src/mod.ts"; + +const CRATE_DIR = `${new URL(".", import.meta.url).pathname}example_crate`; + +Deno.test("RNA-seq Linux test", async () => { + const loc1 = `${CRATE_DIR}/rnaseq_1st.json`; + const loc2 = `${CRATE_DIR}/rnaseq_2nd.json`; + + const parsedArgs = await args.parseArgs([loc1, loc2, "--all"]); + const crate1 = new crate.Crate(parsedArgs.loc1); + await crate1.initialize(); + const crate2 = new crate.Crate(parsedArgs.loc2); + await crate2.initialize(); + compare.compare(crate1, crate2, parsedArgs.all, parsedArgs.threshold); +});