Blat parameters for mapping short sequences

clatrinajes · 05-18-2011, 07:33 AM

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

Richard Finney · 05-18-2011, 08:13 AM

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.

clatrinajes · 05-19-2011, 04:28 AM

Thank you for your suggestion but I have read the blat manual and the parameters ussually used doesn´t work.

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05-18-2011, 07:33 AM	#1
clatrinajes Junior Member Location: Madrid Join Date: May 2011 Posts: 2	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

05-18-2011, 08:13 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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.

05-19-2011, 04:28 AM	#3
clatrinajes Junior Member Location: Madrid Join Date: May 2011 Posts: 2	Thank you for your suggestion but I have read the blat manual and the parameters ussually used doesn´t work.