Bowtie default number of mismatches

Question

[akivab2]

Hi,

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

Thanks

[akivab2]

thanks for your help

Answer 1

[le2336]

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