[BioC] How to get the uniquely mapping reads from object of AlignedRead class [ShortRead]?
mtmorgan at fhcrc.org
Mon Oct 19 17:15:48 CEST 2009
Likun Wang wrote:
> Hi all,
> I want to get the uniquely mapping reads from an object of AlignedRead class.
> How can I do this?
It depends a little on what you mean by 'uniquely aligning', e.g.,
identical sequence, identical + / - strand, overlap of identical
You can try
or if that is not to your liking specify your own criteria for subsetting,
u <- !duplicated(position(aln)) & !duplicated(chromosome(aln))
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