I'm using the command blat with
-minScore=60
and my file has all 60 base DNA sequences. They are actually microarray probes.
My version is
$ blat
blat - Standalone BLAT v. 34 fast sequence search command line tool
The documentation further down the screen says
-minScore=N sets minimum score. This is the matches minus the mismatches minus
some sort of gap penalty. Default is 30
How can I possibly be getting any matches less than 60 bases then ?
$ head -n 15 result.psl | cut -f 1,2 -
match mis-
match
---------------
60 0
60 0
58 1
51 0
59 0
58 1
58 1
56 3
55 3
58 1
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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