Hi I am trying to map my small RNA sequencing reads using bowtie. I would like to allow no mismatches in the first 15nt of my read and then 2 afterwards. I was wondering how to do this with the n-alignment tool in bowtie. Because with the -l option I can only species mismatches within the seed region but not outside.

In addition, the following is not clear to me:

If I e.g. give the option

bowtie -n0 -l15 ....

How many mismatches will bowtie allow after the first 15nt? Sorry I couldn't find anything about this in the manual.

Thanks a lot Anna