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Old 11-18-2009, 07:41 AM   #4
Location: Kansas City

Join Date: Oct 2009
Posts: 88

Apologies, you are correct.

I found that the following settings work for finding sequences smaller than 20 base pairs in length. Although it works, I'm not sure if I would recommend it. I was processing a file for days and eventually ended the processing and took a recommendation to use Bowtie instead.

command line:
blat database query -minScore=0 -tileSize=6 -stepSize=1 -fine output.psl

Unless you have a fairly small set of data to run I would not recommend using these settings unless you have a lot of time to process the files.
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