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Old 11-08-2015, 01:39 AM   #5
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

We've occasionally seen some really odd results with hisat2 that looked more as expected with other aligners (namely, BBMap), so as Brian said give that a try. I've begun suspecting that there are a few bugs that need worked out in hisat2 still.
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