libmelo / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

Snakemake workflow: rna-seq-star-deseq2

This workflow performs a differential gene expression analysis with STAR and Deseq2.

Personally modified version to apply for custom genomes

Tips:

1. Fix some bugs and add some tips in the configs and workflows.
2. Disable some steps, because custom genome may not have uniform Gene Symbol.
3. The custom genome and annotation should be put in resources/genemone.fasta and resources/genemone.gtf in advance.
4. If you can't get access to the wrappers from github like me, you can download the wappers(versions:0.77.0 and 0.75.0) and put them in the homedir and rewrite the wrappers in the workflows as file://wrapper/0.77.0/bio/star/align.

Usage

The usage of this workflow is described in the Snakemake Workflow Catalog.

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