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Old 07-29-2015, 04:41 AM   #4
Location: USA

Join Date: Jun 2012
Posts: 23

For me, it was an issue with IGV. When I looked more closely IGV was coloring nucleotides as being mismatched, but they really were not mismatched. I never found a workaround/explanation, so I just had to ignore all of the claimed mismatches.

Bowtie was mapping properly with zero mismatches allowed.
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