[Genome] running in-house version of blat - Standalone BLAT v. 30

[Thomas Nordahl Petersen]

Hi

I have a problem with a downloaded in-house version of blat. I simply
can not make it run.

I have a database of hg18 (tried database as fasta-file and a .2bit
file) and a small piece of EST sequence, just to test how it works.
This is my command:

blat hg18.2bit test.fasta -t=dna -q=dna

I simply gets a list of all the options when I start that command. Do
you have any idea what I'm doing wrong.
Also, where can i obtain an 11.occ file ?

Hope you can help me.


Sincerely

Professor, Ph.D.
Thomas Nordahl
Technical University of Denmark

[Hiram Clawson]

Good Morning Thomas:

Please note the arguments to blat in its usage message:

blat - Standalone BLAT v. 33x5 fast sequence search command line tool
usage:
blat database query [-ooc=11.ooc] output.psl
where:
database and query are each either a .fa , .nib or .2bit file,
or a list these files one file name per line.
-ooc=11.ooc tells the program to load over-occurring 11-mers from
and external file. This will increase the speed
by a factor of 40 in many cases, but is not required
output.psl is where to put the output.

In your example it looks like you are missing the output.psl argument.
If you want the output to go to stdout, use the special name of "stdout"
in place of the output.psl file name.

You can make your own ooc file:
blat hg18.2bit /dev/null /dev/null -tileSize=11 -makeOoc=11.ooc
-repMatch=1024

If you would like to use the latest version of the source tree, see
also:
http://genome.ucsc.edu/admin/cvs.html

--Hiram