Bowtie2 exact match with one ambiguous character

Question

[nurit.assia]

Hi everyone, I am trying to align a short sequence (23nt) using Bowtie2. My goal is to find an exact match except for one ambiguous character (N) in the sequence, for example CCNGTGGGTTAGA. I used --score-min 'C,0,-1' but I think this causes a problem with accepting the N (since the ambiguous character is not a "match"). Any ideas? Thanks!

Answer 1

[Brian Bushnell]

You can do this with BBMap:

bbmap.sh in=query.fa ref=ref.fa out=mapped.sam strictmaxindel=0 subfilter=0 k=11

This requires all bases to match except the ambiguous one. Depending on the kind of output you need you can also do similar things with BBDuk.

[nurit.assia]

Thanks Brian! I will look into BBMap. Nurit.