bowtie2 --score-min how to input function

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.

bowtie2

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updated 11.7 years ago by Devon Ryan

• written 11.7 years ago by jyu429

1 answer

--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...

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written 11.7 years ago by Devon Ryan

Thank you very much!

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written 11.7 years ago by jyu429

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