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7.9 years ago
anna.coenenstass
•
0
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
