perfect match with bowtie/bowtie2

[jason_ARGONAUTE]

Hi guys,

I have clean small RNA sequencing data at my hands. I wanna perform a perfect-match of miRNA to hairpin data from miRBase with Bowtie. However, i'm confused with its two mapping modes -n & -v. Can anyone tell me the difference of these two modes? Which option fits my case best? why?

Here is my code, for now.
bowtie -p 2 -v 0 hairpin -f sample_1.fa sample_1.bout
The reason i choose -v mode is that i donnt understand the Maq strategy which -n mode adopt, thus i donnt know best options <-n -l -e> settings in my case.

[bw.]

-n mode only considers mismatches in part of the read sequence (in the seed). Also, it takes the base quality scores into account when deciding what is the best alignment.
(See point 2. here)

-v 0 is right for finding exact matches.

[dpryan]

With bowtie2, you can either just use "grep AS:i:0" to get only perfect matches or just use the "--score-min 'C,0,-1'" option, which should do effectively the same thing.