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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