Does anyone know the setting of the bowtie2 parameter to not to allow any mismatch at all?
-N 0 does not work, maybe because it controls only seed length but not entire read length. Also -L i.e. seed length value does not go beyond 35, So I cannot set it to equal to read length (50 in my case). These results in several of the mismatches in my sam output even with -N 0 and -L 22 (default).
I also did not understand the role of --score-min especially, Constant (C) function. There is no example in the bowtie2 manual for constant function. Is it possible with --score-min to control mismatches?
It would be a great help if somebody has experience on this and can suggest me something.