Bowtie default number of mismatches

Hi,

Is there a default number of mismatches when not specifying the number of mismatches in Bowtie?

Thanks

bowtie alignment mismatches

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updated 10.9 years ago by Biostar

• written 11.1 years ago by akivab2

thanks for your help

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written 11.1 years ago by akivab2

1 answer

By default, Bowtie is set to tolerate up to 2 mismatches in the first 28 bases on the left end (the "seed") of the read.

http://bowtie-bio.sourceforge.net/manual.shtml#the-bowtie-aligner

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updated 6.8 years ago by Ram

• written 11.1 years ago by le2336

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