featureCounts Refseq Fix for bacteria

[Groshack]

Hi everyone,

Thank for so much for writing RNA-Seq by Example. I am new to all this and this book has been a life saver. I just want to post my fix to Subread's FeatureCounts when using RefSeq.gtf files. In my situation FeatureCounts was finding 76/1996 features of my prokaryotic organism.

I amended the code to find the feature 'gene' and it worked.

Original line:
featureCounts -p -a refs/features.gff -o counts.txt bam/BORED_?.bam bam/EXCITED_?.bam

featureCounts -p -F GTF -t 'gene' -a refs/refseq.gtf -o counts.txt bam/1_?.bam bam/2_?.bam

I hope this finds someone in need!

Cheers,
Groshack

[ialbert]

Thanks for the note, I will merge this recommendation into the book in the near future

[Groshack]

You're a champion!