- Cellecta guides for new kits

- minor typos fixed

docs/mixcr/guides/cellecta-air-tcr-bcr/scripts/020-upstream-preset.sh

@@ -1,4 +1,4 @@
 mixcr analyze cellecta-human-rna-xcr-umi-drivermap-air \
 	raw/Sample1_R1.fastq.gz \
-	raw/Sample1_1_R2.fastq.gz \
+	raw/Sample1_R2.fastq.gz \
 	results/Sample1

docs/mixcr/guides/cellecta-human-dna-xcr-umi-drivermap-air.md

@@ -0,0 +1,117 @@
+# DriverMap Adaptive Immune Receptor (AIR) DNA TCR-BCR Profiling
+
+Easy-to-run, single-day assay that uses multiplex PCR-NGS technology to profile T-cell receptor (TCR) or B-cell receptor (BCR) repertoire present in human DNA. The DriverMap AIR DNA assay measures the frequency of CDR3 clonotypes to quantify the clonal frequency of T and B cells.
+
+Bellow you can see the structure of cDNA library.
+
+![](../reference/pics/cellecta-human-dna-xcr-umi-drivermap-air-light.svg#only-light)
+
+![](../reference/pics/cellecta-human-dna-xcr-umi-drivermap-air-dark.svg#only-dark)
+
+The data for this tutorial consists of one sample prepared according to the manufacturer's protocol.
+
+All data may be downloaded using the script bellow.
+
+??? tip "Use [aria2c](https://aria2.github.io) for efficient download of the full dataset with the proper filenames:"
+    ```shell title="download.sh"
+    --8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/010-download-aria2c.sh"
+    ```
+    ```shell title="download-list.txt"
+    --8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/download-list.txt"
+    ```
+## Upstream analysis
+
+MiXCR has a dedicated preset for this protocol, thus analysing the data is as easy as:
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/020-upstream-preset.sh"
+```
+
+Running the command above will generate the following files:
+
+```shell
+> ls result/
+
+# human-readable reports 
+Sample1.align.report.txt
+Sample1.align.report.json
+Sample1.refine.report.txt
+Sample1.refine.report.json
+Sample1.assemble.report.txt
+Sample1.assemle.report.json
+
+# raw alignments (highly compressed binary file)
+Sample1.vdjca
+
+#Alignments with corrected barcode after ```mixcr refineTagsAndSort```
+Sample1.refined.vdjca
+
+# TCR and BCR CDR3 clonotypes (highly compressed binary file)
+Sample1.clns
+
+# TCR and BCR CDR3 clonotypes exported in tab-delimited txt
+Sample1.clones_IGH.tsv
+Sample1.clones_IGK.tsv
+Sample1.clones_IGL.tsv
+Sample1.clones_TRAD.tsv
+Sample1.clones_TRB.tsv
+```
+
+While `.clns` file holds all data and is used for downstream analysis using [`mixcr postanalisis`](../reference/mixcr-postanalysis.md), the output `.txt` clonotype table will contain exhaustive information about each clonotype as well:
+
+??? tip "See Sample1.clones_IGH.tsv clonotype table"
+    {{ read_csv('docs/mixcr/guides/cellecta-human-dna-xcr-umi-drivermap-air/figs/Sample1.clones_IGH.tsv', engine='python', sep='\t') }}
+
+
+## Quality control
+
+Now let's look at the QC plots. That can be easily done using [`mixcr exportQc`](../reference/mixcr-exportQc.md)
+function.
+
+First we will look at the alignment report:
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/070-qc-align.sh"
+```
+
+![align QC](cellecta-human-dna-xcr-umi-drivermap-air/figs/alignQc.svg)
+
+From this plot we can tell that all samples have high alignment rate and nearly 90% of all reads from each sample have been successfully aligned to the reference sequences and CDR3 has been established. 
+
+Now we can check chains distribution plot:
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/080-qc-chainUsage.sh"
+```
+
+![chain usage QC](cellecta-human-dna-xcr-umi-drivermap-air/figs/chainUsage.svg)
+
+Finally, we can take a look at the reads per UMI distribution.
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/090-qc-tags.sh"
+```
+
+![tags QC](cellecta-human-dna-xcr-umi-drivermap-air/figs/tags.0.svg)
+
+
+## Reports
+Finally, MiXCR provides a very convenient way to look at the reports generated at ech step. Every `.vdjca`, `.clns` and `.clna` file holds all the reports for every MiXCR function that has been applied to this sample. E.g. in our case `.clns` file contains reports for `mixcr align` and `mixcr assemble`. To output this report use [`mixcr exportReports`](../reference/mixcr-exportReports.md) as shown bellow. Note `--json` parameter will output a JSON-formatted report.
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/100-qc-exportReports.sh"
+```
+
+```shell
+--8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/scripts/101-qc-exportReports-json.sh"
+```
+
+??? "Show report file"
+    === "`.txt`"
+        ```shell
+        --8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/figs/Sample1.report.txt"
+        ```
+    === "`.json`"
+        ```json
+        --8<-- "guides/cellecta-human-dna-xcr-umi-drivermap-air/figs/Sample1.report.json"
+        ```