Blat is an alignment tool similar to BLAST (BLAT = BLAST Like Alignment Tool). Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments
Run blat without any command line arguments to display all options
ibestadm@fortytwo ~/module_tests/blat $ module load blat
ibestadm@fortytwo ~/module_tests/blat $ blat
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.
...
Simple case
cd
wget http://www.hpc.uidaho.edu/examples/blat_example.tar.bz2
tar -xf blat_example.tar.bz2
cd blat_example
module load blat
blat species.fa short_seqs.fa blat_out1.psl
Now make the ooc file to speed things up
blat species.fa /dev/null /dev/null -makeOoc=11.ooc -repMatch=1024
and run blat using the file
blat species.fa short_seqs.fa -ooc=11.ooc blat_out2.psl
We also have a BLAT install compiled with FastQ file support (used by default with ARC)
module load blat-fastq