Bowtie1 Options For Mirna
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7.7 years ago
Varun Gupta ★ 1.2k

Hi I am using a data set with 36 bp read sequence. I am using bowtie1 to align it to human genome. Since I am interested in miRNA and those are generally 21-23 bp long, is there a way in bowtie1 that if I specify seed length -l 25 with n option as 2 then if the first 25 bp matches the genomic seq with 2 mis matches and remaining bases does not match, just drop the remaining bases and report the matched 25bp.

If not is there a way I can perform such alignment.

Hope to hear from you soon. Regards Varun

mirna • 1.6k views
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Entering edit mode
7.7 years ago
Ido Tamir 5.2k

If you insist on doing your own pipeline you could use bowtie2 with local alignment or remove the adaptor with one of the many tools that do this.

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7.7 years ago
Martombo ★ 2.9k

My advice would be to use one of the existing tools for miRNA, like miRDeep2.

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