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Old 05-18-2011, 07:33 AM   #1
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Location: Madrid

Join Date: May 2011
Posts: 2
Default Blat parameters for mapping short sequences

Dear all, Anybody knows which are the parameters for mapping sequences that are between 19 to 30 nucleotides? I'm using blat aligner program that I have only obtained location for the sequences that are 30 nucleotides long. I have used a tilesize=11 and stepsize=4. My data contains sequences of size between 16 and 32 nucleotides and also I would like to locate sequences within 30 nucleotides.
Thank you for your help
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