Hi, I want to ask if HTSeq-count will over-counts the reads in overlapped exons?
IF I give the refseq.gtf as gtf annotation, there should be some isoforms overlap exons, so how htseq-count handle this.
I think htseq-count will give counts for each isoform separately.
And I calculate rpkm for each isoform by myself.
And then, for one gene have many isoforms, I calculate the average rpkm for this gene. Is this procedure OK?