Snakemake-rnaseq

This is a Snakemake workflow for generating gene expression counts from RNA-sequencing data using STAR and featureCounts (from the subread package). The workflow is designed to handle both single-end and paired-end sequencing data, as well as sequencing data from multiple lanes. Processing of patient-derived xenograft (PDX) samples is also supported, by using disambiguate to separate graft/host sequence reads.

If you use this workflow in a paper, don’t forget to give credits to the authors by citing the URL of this repository and, if available, its DOI (see above).