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

Martin Morgan mtmorgan at fhcrc.org
Fri Aug 12 05:34:03 CEST 2011

On 08/11/2011 09:50 AM, Kunbin Qu 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.

ShortRead::tables() could be used for exactly identical unaligned reads. 
ShortRead::occurrenceFilter is an implementation for non-gapped, aligned 
reads. For aligned reads with gaps I think you're on your own, but maybe 
GRanges::readGappedAlignments or Rsamtools::scanBam + the logic of 
ShortRead::occurrenceFilter would be a starting point. Perhaps your 
aligner has already flagged duplicate reads, in which case the 'flag' 
field available in scanBamParam and scanBam would be helpful.

Hope that is of some help.


> -Kunbin
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