bowtie2 --score-min option

Question

[biolab]

Hi everyone,

I am using Bowtie2 to perform 20-bp sequence alignment. I need to find minimum of 15-bp matched sites, in other words, the length of mapped sites >=15bp. No gaps are allowed.

When reading bowtie2 manual, I can't well understand the --score-min option. If I choose the constant (C) method, is --score-min=C,-30,0 ok for my work? Hope experts give me some advices. THANK you very much!

Answer 1

[Devon Ryan]

If you need to disallow gaps, then just set the gap penalty to a high value: --rdg 60,3 --rfg 60,3. It's likely that you want --local alignment, where the default score-min is ~44. In order for a 15 base alignment with the other 5 bases soft-clipped to be considered valid, the match bonus would need to be at least 3 (--ma 3). The simplest method to then allow mismatches for the other 5 bases would be to not use a mismatch penalty (--mp 0,0).

BTW, you might have better luck with bowtie1, since it doesn't do gapped alignment and allows somewhat different specification of permitted matches.

[biolab]

Thank you very much, Devon. I am further reading the manual and testing the local, ma and mp options.