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Old 05-18-2011, 06:33 AM   #1
clatrinajes
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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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Old 05-18-2011, 07:13 AM   #2
Richard Finney
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This might help :
http://genome.ucsc.edu/FAQ/FAQblat.html#blat8

Please note:
http://genome.ucsc.edu/goldenPath/he...html#BLATAlign
BLAT is designed to quickly find sequences with 95% or greater similarity of length 25 bases or more

You might want to use BWA or Bowtie, instead.
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Old 05-19-2011, 03:28 AM   #3
clatrinajes
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Thank you for your suggestion but I have read the blat manual and the parameters ussually used doesn´t work.
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