Mismatches In Bowtie
1
0
Entering edit mode
8.2 years ago
roll ▴ 330

Hi,

I am trying to understand bowtie mismatch option -v I have this sequence of 16bp and I try to match it in the whole genome. First i tried -v 0 and then -v 1 With -v 1 i would expect that there would be 1 mismatch in the output. But when i looked at the output of bowtie (column5) it all seems the same - no mismatch. So what is actually happening? Am i looking at the wrong column?

Best,

bowtie alignment • 3.3k views
ADD COMMENT
1
Entering edit mode
8.2 years ago

-v option is for maximum allowed mismatch.

If there is a better match, it will be reported.

If you specify --best --strata option, then only the best alignments will be reported.

ADD COMMENT
0
Entering edit mode

Thank you. That is great

ADD REPLY

Login before adding your answer.

Traffic: 984 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