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?
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.