[Bioc-sig-seq] assess how many duplicated reads

Sean Davis sdavis2 at mail.nih.gov
Thu Aug 11 19:34:50 CEST 2011

The picard library (java-based) is a very useful library for doing
this type of thing.  This can be done in R, but the picard folks have
put a lot of thought into how to find and mark duplicates including
optical duplicates.  This is particularly true if you have paired-end


On Thu, Aug 11, 2011 at 12:50 PM, Kunbin Qu <KQu at genomichealth.com> wrote:
> Hi, I have some human single end RNA-seq runs on HiSeq. Can I have some suggestions on how to assess how many duplicated reads out of these libraries? I looked around srFilter() in ShortRead, but have not had a clear thought on how to implement it? Should I use IRanges as an alternative to assess the unique starting site after the mapping? If so, what function do you suggest? I'd like to count reads which map to the same location (even with some mismatches) as duplicates. Thanks.
> -Kunbin
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