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yichizhng / bwt

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Scoring quirks #2

Open yichizhng opened 10 years ago

yichizhng commented 10 years ago

I use Bowtie's scoring scheme of -5 affine gap penalty, -3 for gap extend, -6 for mismatch; unfortunately this leads to some nonsense like 3 read deletions scoring higher than three mismatches. Higher affine gap penalty might help?

yichizhng commented 10 years ago

Rather, higher penalty for read deletions