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Old 11-05-2013, 12:15 AM   #1
Location: china

Join Date: Aug 2013
Posts: 14
Default perfect match with bowtie/bowtie2

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.
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