Open yichizhng opened 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?
Rather, higher penalty for read deletions
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?