Question: Bowtie1 Options For Mirna
gravatar for Varun Gupta
5.6 years ago by
Varun Gupta1.1k
United States
Varun Gupta1.1k wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 5.6 years ago by Varun Gupta1.1k

my advice would be to use one of the existing tools for miRNA (, like miRDeep2 (

ADD REPLYlink written 5.6 years ago by Martombo2.5k
gravatar for Ido Tamir
5.6 years ago by
Ido Tamir5.0k
Ido Tamir5.0k wrote:

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.

ADD COMMENTlink written 5.6 years ago by Ido Tamir5.0k
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