I am using Bowtie2 to map small RNA reads (not microRNAs) to the genome. To account for allelic divergence, I need to set it to allow 1 or maybe even 2 mismatches. Is it possible to change that? I believe the N -1 option only lets you allow mismatches in the seed region.
I am using end-to-end very sensitive option.
Thanks for any insights.
I am using end-to-end very sensitive option.
Thanks for any insights.
Comment