Say, I'm aligning, with Bowtie2 default settings, this short read:
to this short reference:
The read is a bit longer than the reference. The problem: Bowtie aligns it resulting in this CIGAR string: 36M5I4M Which looks like:
reference:AGTGATCAGTGGTACACCATGTACGAATTCTCGCCT GCGA read: AGTGATCAGTGGTACACCATGTACGAATTCTCGCCTGCGAGACGA
Bowtie2 'made up' an insertion only for the purpose to fit the whole read on the reference. But I want to allow for the read to extend the reference (perhaps assign a penalty to it, but not throw in a insertion just like that). How do I do that? Can't seem to find it anywhere.
Many thanks in advance!