How Does Htseq Handle Duplicated Rna-Seq Reads?

Question

[ccshao]

Hi,

I guess the htseq-count use duplicated reads (identical location) when do counting, is it true? Didn't found a clear answer on the web.

Thanks.

Answer 1

[Devon Ryan]

Yes, it counts them. Particularly with highly expressed genes, you're quite likely to observe what would otherwise be termed PCR duplicates that aren't actually duplicates.

[ccshao]

Thanks for the quick answer. I knew there are different opinions on wether removing these reads. I kept them. However, it maybe a problem in single cell? Do you any experience on it?

[Devon Ryan]

I unfortunately don't have any personal experience with single-cell data, which is definitely a bit of a different beast than regular RNAseq. It seems that how big of an issue the duplicates are in single-cell data is somewhat method dependent. You might try with and without duplicates and see if this makes a noticeable difference.

[ccshao]

Thanks for your comments.