CDS read counts per gene

Question

[ashkan]

Hi Guys,

I have aligned RNA-seq data and have bam files. I am goint to coundt the number of reads per gene but I need only the number of reads per gene only for coding sequence part of genes. do you guys know how to get those counts? tHANKS

[Farbod]

Dear Behzad, Hi

Does this post can offer any helps to you ?

And I guess if you have GTF file there would be some transcripts coordinates such as CDS in it.

~Best

[WouterDeCoster]

If I understand correctly, he needs counts, not reads. This is exactly what featureCounts or htseq-counts does. "Counting reads per annotation element".

[Farbod]

Dear @Wouter, Hi.

Do you mean this and this ?

[WouterDeCoster]

Yes, as such he can "count the number of reads per gene" -> as he asked for ;-)