RNA/ATAC Seq QC Reporter

R functions and scripts for summarizing and performing sample-level QC on sequencing pipeline data.

Contents

Dependencies

Installation

Available Reports

Running Reports

NGS Batch Report

• Parameters
• Sample Sheet Guidelines
• Outputs
• Tests

Version History

Dependencies

This repository requires that pandoc and libhdf5-devel libraries are installed as dependencies of the H5MANIPULATOR functions:

sudo apt-get install pandoc libhdf5-dev

CRAN packages can be installed in R using:

# Example
install.packages("jsonlite")
install.packages("rmarkdown")
install.packages("optparse")

H5MANIPULATOR, Because it is a private repository, you may need to provided a Github Personal Access Token for installation:

Sys.setenv(GITHUB_PAT = "[your_PAT_here]")
devtools::install_github("bwh-bioinformatics-hub/H5MANIPULATOR")

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Installation

qcreporter is an R package with associated executable scripts. First install dependencies. Then install the R package from Github repository:

Sys.setenv(GITHUB_PAT = "[your_PAT_here]")
devtools::install_github("bwh-bioinformatics-hub/qcreporter")

To run scripts, clone the GitHub repository and run the desired wrapper script within the local clone.

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Available Reports and Scripts

Available batch reports are as follows:

• scRNA cell report: Batch report for stand alone scRNA

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Input Parameters

There are 9 parameters for this script:

• -b or --experiment: The experiment name, ie B001
• -i or --in_dir: The input directory containing the files to process. Should include the following subdirectories:
  • h5: Contains all sample .h5 files for the batch generated by tenx_rna_metadata_update
• -k or --in_key: A 6-column .csv Sample Sheet (see format below) of identifiers for all samples in the batch.
• -n or --n_cores: An integer value of number of cores to use for multithreaded processes, used by Seurat functions
• -m or --mc_mb_limit: An integer value of number of maximum size in Mb allowed for exporting globals to each worker in multicore processing (for futures R package). Defaults to 50000, suggest >= 20000.
• -d or --out_dir: A directory path to use to output the batch report.
• -o or --out_html: A filename to use to output the HTML summary report file. For example "B001_scRNA_batch_report.html"

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RNA-Seq Sample Report

The qc_batch_summary.r wrapper script renders `qc_report_rna_seq.rmd to create a RNA-Seq Sample QC report (html).

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Input Parameters

There are 8 parameters for this script:

• -b or --batch_id: The experiment name,
• -m or --in_method: A ";"-delimited string of the data streams being processed enclosed in quotes, for example "scrna"
  • scrna (single cell RNA)
• -i or --in_dir: The input directory containing all results files to process. Must include one subdirectory per modality named in in_method above.
• -k or --in_key:
• -d or --out_dir: A directory path to use to output the batch report.
• -o or --out_html: A filename to use to output the HTML summary report file. For example "experiment_id_scRNA_report.html"

An example run:

git clone https://github.com/acicalo2/rna_atac_seq_qc_reporter.git

Rscript --vanilla \
    /home/jupyter/batchreporter/qc_batch_summary.r \
    -e experiment_id  \
    -m 'scrna;scatac' \
    -i /home/acicalo/output/scrna \
    -k /home/acicalo/samplesheet/samplesheet.csv   \
    -d /home/acicalo/output/ \
    -o  experiment_id_rnaseq_sample_report.html 
    ```

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<a id="rnaseq_report_out"></a>

#### Output Files

`qc_batch_summary.r` will generate the HTML reporting file with name as defined by input parameter -o. 

experiment_id_rnaseq_sample_report.html

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#### Version History  

|Version|Date|Description|
|--------|---------|------------------------------------------------|
|1.1.0|01/12/2023|Addition of sample report|
|1.0.0 |          |Initial release, scRNA |  


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