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Old 10-16-2015, 07:04 PM   #1
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Default map with defined number of mismatches


how can I map reads against the reference genome, so that I'm sure they align continuously, but allowing from 0 to 5 mismatches in the alignment?
Or alternatively find in the alignment, reads that map with 0 to 5 mismatches?
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Old 10-16-2015, 09:20 PM   #2
Brian Bushnell
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BBMap has a "subfilter" flag - e.g. "subfilter=5" - which will ban alignments with more than 5 mismatches. It's a global aligner, so the reads will align continuously.
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