HTseq feature count handling of transcripts with shared exons?

Question

[dk0319]

I am curious to know how htseq will assign a read to a particular transcript if said read maps to a shared exon between two isoforms? If anyone has any experience with this or can offer any insight it would be greatly appreciated. Thank you in advance.

Answer 1

[i.sudbery]

HTseq can only count at a gene level, not a transcript level, for precisely this reason.

[dk0319]

Thank you, this is what I suspected but I wanted a second opinion!