Entering edit mode
7.2 years ago
nurit.assia
•
0
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!
Thanks Brian! I will look into BBMap. Nurit.