Blat parameters for mapping short sequences

[clatrinajes]

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]

This might help :

http://genome.ucsc.edu/FAQ/FAQblat.html#blat8

Please note:

http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.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]

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