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Old 07-24-2014, 05:26 AM   #4
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Join Date: Aug 2011
Posts: 106

Maybe, when you are doing the mapping, you are getting mismatches in the 'GG' which is resulting in the lower number of hits. Not sure if it's possible, but maybe there is a way to tell BWA to allow 4 mismatches, but the last 'GG' has to be fixed and no mismatches allowed in those 2 bps. This way, the only mismatches are in the rest of the fragment.

Another thought would be that you would want to potential search the genome for the 'NGG' sequence first, then see if the rest of your sequence can align following that location with allowing the up to 4-mismatches.
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