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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