Entering edit mode
10.1 years ago
ccshao
▴
10
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.
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?
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.
Thanks for your comments.