counting the reads mapped only to the coding sequence

Question

[alirezamomeni707]

I have aligned the RNAseq data to the transcriptome and have .bam files. now I want to count the reads that map to the coding sequence not the whole transcriptome. I usually use HTseq count to do so. do you guys know how to do that?

[WouterDeCoster]

I usually use HTseq count to do so.

So what's the problem then? Seems you already know the solution.

Answer 1

[VHahaut]

Did you look at this answer?

Question: htseq counts on genes (introns + exons)

Answer 2

[h.mon]

Why don't you tell exactly what you did - commands included?

Usually, when reads are aligned to a transcriptome, one uses RSEM or eXpress (or some other expectation-maximization algorithm) to perform quantification of transcript expression.

Now, in case you aligned to the genome and have a gene annotation, you can use HTSeq or (better) featureCounts to perform quantification of gene expression.