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Old 02-07-2014, 03:49 AM   #6
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You might try quality trimming things to see if that solves the problem. Alternatively, try blasting a few reads and see how they align. It may be that you simply need to change the defaults for bowtie (e.g., score-min).
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