Default number of mismatches in bowtie -v alignment mode?

Question

[lbro]

I cannot for the life of me figure out what the default number of allowed mismatches is when running bowtie (not bowtie2) in -v mode. The manual clearly states that it's 2 for -n mode, but I cannot find out for -v mode.

Can anyone educate me? Thanks

[andres.firrincieli]

Hi Ibro,

I could be wrong but you do not have a default setting for -v mode. From the manual:

In -v mode, alignments may have no more than V mismatches, where V may be a number from 0 through 3 set using the -v option.

Therefore in -v mode you must specify the number of allowed mistmatches. If you look at the usage:

-v <int> Report alignments with at most <int> mismatches. -e and -l options are ignored and quality values have no effect on what alignments are valid. -v is mutually exclusive with -n.

-n/--seedmms <int> Maximum number of mismatches permitted in the “seed”, i.e. the first L base pairs of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the default is 2. This option is mutually exclusive with the -v option.

Answer 1

[lbro]

Hi Andres, thank you for your input. I'm just puzzled, because bowtie runs just fine for me without specifying any V in -v mode... That's why I figured that there must be a default value that I just didn't know what was, just like 2 for -n mode.