SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Blat parameters for mapping short sequences (http://seqanswers.com/forums/showthread.php?t=11451)

clatrinajes 05-18-2011 06:33 AM

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

Richard Finney 05-18-2011 07:13 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 03:28 AM

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


All times are GMT -8. The time now is 06:56 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.