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. Accoring to 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!