rnaseq

Basic perl script to align RNA-seq single-end fastq files with STAR and then extract transcript counts with featureCounts/subread. This is designed to be a convenience for RNA-Seq processing, and to save time writing scripts.

options

-a annotation file for featureCounts. Accepts file afterward. Optional.

-d debug. Only print commands that would be executed. Does not accept arguments. Optional.

-g genome directory for STAR alignment. Accepts directory as argument. Required.

examples

specify an annotation file and a STAR genome directory

perl rnaseq.pl -a ~/GENE_DATA/gencode.v26.annotation.gtf -g ~/GENE_DATA/hg38

only do debugging, just to see the commands that rnaseq.pl will output

perl rnaseq.pl -a  ~/GENE_DATA/gencode.v26.annotation.gtf -g ~/GENE_DATA/hg38 -d