Bowtie -m and -v parameter equivalent in bowtie2?

Question

[datascientist28]

Quick question but I'm starting a new project with larger read lengths, so I'm switching from bowtie1 to bowtie2. I've been reading the bowtie2 manual and can't seem to find the equivalence of -m and -v in bowtie2. According to the bowtie1 manual:

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

-m - instructs bowtie to refrain from reporting any alignments for reads having more than 3 reportable alignments

Does anyone know the equivalent parameters in bowtie2?

(Background of project: running an alignment in Dogs and have low alignment rate (~50%) and think maybe the low align rate is due to variability in dog breeds (CanFam3.1 is boxer). We are going to try and alter the above parameters to see if it can help the alignment rate)

Any help is appreciated!

Answer 1

[Devon Ryan]

There's no equivalent of those parameters. Instead, you'll want to change the --score-min option (and possibly use local alignment).