I'm wondering what "some sort of gap penalty" refers to. Also I query
25bp sequence using the default, BLAT still gives the result. By
definition 25bp sequence should at most have a score of 25, which is
less than 30. Why the query still returns the the result?
-minScore=N sets minimum score. This is the matches minus the
mismatches minus some sort of gap penalty. Default is 30
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Regards,
Peng
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