Is HTseq result based on uniquely mapped reads?

Question

[biolab]

Dear all,

I heard from one of my colleague that HTseq result is based on uniquely mapped reads. Is that true? I think this point needs to be clarified, because HTseq-edgeR has been widely used for gene expression quantification. I appreciate any of your comments. THANKS!

Answer 1

[Matt Shirley]

See the second question in the "FAQ" section for the htseq-count documentation.

[biolab]

Hi, Matt, the answer is very helpful!

[Kevin Blighe]

Update 20th September 2018:

Now moved here for anybody else arriving here:

• https://htseq.readthedocs.io/en/master/count.html