Processing of scRNAseq FASTQ

Snakemake pipeline to process FASTQ files from 10x Genomics using CellRanger or PIP-seq data using pipseeker. Each sample will be submitted as a single job to run simultaneously.

Cellranger Input: config.yaml

• FASTQ_DIR - path to folder where fastq files are located
• SAMPLE_ID - list sample IDs (must match name prefix in fastq files e.g. _S1_L001_R1_001.fastq.gz)
• KEEP_BAMS - whether to keep large intermediate BAM files for other analyses (default: no)

https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-gex-count

Pipseeker Input: config.yaml

• STAR_INDEX_PATH - path to STAR aligner index file
• SAMPLE_ID - list sample IDs (must match name prefix in fastq files e.g. _S1_L001_R1_001.fastq.gz)
• CHEMISTRY_VERSION - chemistry version v4 or v5

How to run in respective folders:

snakemake --profile lsf

Pending:

• Merge pipelines into one and add input functions to decide which tool to run