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

[Martin Morgan]

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.

Martin


>
> -Kunbin
>
>
>
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