Neither should be marked as a duplicate,
N
On Mon, Mar 30, 2015 at 3:42 PM, Faith Coldren <fcold...@mail.med.upenn.edu>
wrote:
> Hi,
>
> Thanks for the reply. If the 3' coordinate differs for two pairs that have
> the same 5' genomic coordinate, will one of them be marked as duplicates?
>
> As in the case of:
>
> ----------R1------------->
> <---------------R2----------------
>
> ----------R1------------->
> <---------------R2----------------
>
> Thanks,
> Faith
>
>
> On Thu, Mar 5, 2015 at 1:21 PM, Nils Homer <nho...@broadinstitute.org>
> wrote:
>
>> 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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>>
>
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