I am using Bowtie 2 for an interspecific alignment (specifically between two fungus gnat/Sciarid species). I am mapping pair-end Illumina reads to an Illumina genome assembly.
The default maximum and minimum mismatch penalties are 2 and 6, but I am aware that I may need to change these given that I am doing an interspecific alignment. However I've never used Bowtie before and have no idea what to change them to. Does anyone have experience using Bowtie 2 for interspecific alignments and could recommend which maximum and minimum mismatch penalties to use?
Thanks in advance.