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Old 11-06-2009, 11:36 AM   #1
Location: Kansas City

Join Date: Oct 2009
Posts: 88
Default BLAT settings for 17bp sequences?

Hello everyone,

I am trying to align 17bp sequences to a genome using the command line version of BLAT and was wondering if anyone could help me out on the proper settings for these particular sequence lengths? I have tried the default settings and -tileSize=6 -stepSize=1, both resulted in no or very few (<20) alignments.

Any help on this would be greatly appreciated.

Thanks in advance,
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