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Old 11-06-2009, 10:36 AM   #1
DrD2009
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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,
Brandon
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Old 11-17-2009, 10:45 AM   #2
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Nevermind. I figured it out.
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Old 11-17-2009, 10:28 PM   #3
sklages
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And *what* did you figure out? This might be interesting for people facing the same "problem".
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Old 11-18-2009, 06:41 AM   #4
DrD2009
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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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