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Old 02-26-2015, 10:34 AM   #186
rkanwar
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Location: minnesota

Join Date: Feb 2011
Posts: 8
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Hello Brian,

Thank you for your reply! I was using the read sequence from the SAM record for BLAT, which might explain the same strand.
Is there some easy way to filter out properly mapped PE reads [which have the right orientation and are within the fragment length distribution] which are uniquely aligned ?

Rahul
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