Bowtie1 Options For Mirna

Question

[Varun Gupta]

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

Answer 1

[Ido Tamir]

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.

Answer 2

[Martombo]

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