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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