BLAT

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

website

Examples

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

FastQ BLAT

We also have a BLAT install compiled with FastQ file support (used by default with ARC)

module load blat-fastq