No, neither should be marked as duplicates. We look at the genomic
position of the first base sequenced, which for a read mapped to the
forward strand is the 5' genomic coordinate, and for a reverse strand is
the end of the alignment (3' coordinate). We adjust the coordinate by
considering the clipped bases for good measure.
N
On Thu, Mar 5, 2015 at 10:53 AM, Faith Coldren <fcold...@mail.med.upenn.edu>
wrote:
> Hi,
>
> Let's say two mapped reads pairs have the same 5' starting coordinate, but
> one read has the 0x10 FLAG in the sam file while the other read doesn't
> have the 0x10 FLAG. Or for paired end, the two sets of read pairs have the
> same coordinates but opposite orientations.
>
> Will one of the reads/read pairs be marked as a duplicate by the Picard
> tool MarkDuplicates?
>
> Thank you,
> Faith
>
>
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