Hi
How can I get a read count per exon per transcript in a particular gene from BAM file? I tried using htseq-count
with id_attr=transcript_id
but this approach does not give me the read count per exon per transcript. I tried using DEXSeq to get the read count, but it does not get what I want. Is there any way to get the read count? I only got one gene of interest to analyse which TPM1. This gene has more than 40 isoforms, so it is possible to get each of the isoforms their read count for each exon. Thanks!
I tried but it need 2 bam files which is not the case. I don't want to compare, I just want a read count of each exon for each transcript. I think it quite arbitrary as it quite hard to distinguished which read mapped to which isoform. How do you think?
Paste your exact command, so we can probably see where you might have wrong.