coding sequnce read coun

Question

[ashkan]

Hi Guys, I asked a question yesterday but did not get my answer and I really need it. I have RNA-seq data and its bam file. I want to get the read count per gene. but the problem is that I need only the read counts in the coding sequence part (I don't need the read counts at 5' and 3' UTRs). if I use Htseq And Feature Count I would get the read count for the transcript. do you guys know how I can get the read count per gene only at the CODING SEQUENCE? thanks

Answer 1

[GenoMax]

You could leave only the entries for stuff you want counts on and take the rest of the lines out of your GTF (is that what you are using) file?

Answer 2

[WouterDeCoster]

You could just remove the UTRs from your gtf file... grep -v