Bowtie mismatch settings

Question

[biolab]

Dear all,

I am not an experienced user of Bowtie2. I noticed there are a few settings related to mismatch: -v, -n and -e.

-n is the max mismatches within seed (default 2)

I am confused with -v and -e. According to the manual, -v means end-to-end hits w/ <= v mismatches; -e is the max sum of mismatch quals across alignment for -n (default: 70).

Could anyone explain in a little bit more details for -v and -e? If I want the total mismatch set to 2, which option should I use? I appreciate your help! THANKS!

[PoGibas]

Are you using bowtie or bowtie2? Make sure you're reading correct documentation.

[biolab]

Thanks, Pgibas for noticing me. When running Bowtie2, I found a list of options, but which option is total mismatch? (Note -N is max mismatch in seed) THANKS!

[PoGibas]

• http://seqanswers.com/forums/showthread.php?t=19729
• Mismatch Option In Bowtie2

[biolab]

Thanks a lot, pgibas, I understand filtering SAM is the way to do so.