Bowtie2 scoring translated to number of non matching nt allowed
I ran a paired alignment of 150nt long reds using bowtie2 with the strictest scoring parameter I could find:
--score-min L,0,0
In the manual "The best possible alignment score in end-to-end mode is 0, which happens when there are no differences between the read and the reference."
Given the linear scoring formula is of the form:
f(x) = -0.4 + -0.6 * x
Am I correct in assuming that the score-min parameter I have set will allow only perfect matches between read and reference? (just double checking I am not missing something)
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You could test your hypothesis using a toy example. Extract a small test sequence to create an index, then extract a subsequence to create some test reads, with or without various modifications, and test your alignment parameters.
I just converted the bam to sam and grepped the NM:i: vlalues (Edit distance to the reference) and found them all to be zero.