I am using bowtie2. I would like to use more loose mapping criteria in order to have more reads that are mapping on a particular place (e.g. mitochondrial genome) of the reference, partially and with more than one mismatches. Is there any other parameter that I can check except the maximum fragment length (
-X) that I can give a very large number and the max mismatches in seed alignment (
-N) which as I can see it has to be 0 or 1 (so, only 1 mismatch?)
Thank you very much and I'm sorry for my ignorance.