Question

Bowtie default number of mismatches

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9.4 years ago

akivab2 ▴ 120

Hi,

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

Thanks

Bowtie alignment mismatches • 5.3k views

ADD COMMENT • link updated 9.2 years ago by Biostar 20 • written 9.4 years ago by akivab2 ▴ 120

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thanks for your help

ADD REPLY • link 9.4 years ago by akivab2 ▴ 120

Ram · Accepted Answer · 2015-07-01

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9.4 years ago

le2336 ▴ 70

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.

ADD COMMENT • link updated 5.1 years ago by Ram 44k • written 9.4 years ago by le2336 ▴ 70