bowtie2 --score-min how to input function

Question

[jyu429]

Hi,

I want to use the function f(x) = 20+ 30*ln(x) for my function when I do local alignment in bowtie2 with the --score-min option. I can't seem to get the syntax right in the command line. Can someone give me an example? Thanks.

Answer 1

[Devon Ryan]

--score-min G,20,30

Edit: BTW, you'll have to tweak the match/mismatch scores to get that to work. I really can't give any guarantees on the quality of alignments those would then produce...

[jyu429]

Thank you very much!