Bowtie mismatch settings
0
0
Entering edit mode
6.9 years ago
biolab ★ 1.3k

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.  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!

 

bowtie mismatch • 5.2k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2510 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6