Bowtie1 Options For Mirna · Biostar

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Bowtie1 Options For Mirna

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

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updated 5.7 years ago by Biostar

• written 12.4 years ago by Varun Gupta

2 answers

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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written 12.4 years ago by Ido Tamir

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

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updated 5.7 years ago by Ram

• written 12.4 years ago by Martombo

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