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Old 07-18-2016, 10:52 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Bit 2 denotes aligning as a "proper pair according to the aligner". Firstly, the alignments point away from each other. Secondly a 3kb fragment size is about 6-10x wider than expected. Are these mate-pair alignments? If so, you'll need to tell the aligner that.
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