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