HPC:BLAT

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BLAT

UCSC's BLAT is installed across all HPC nodes.

Usage

BLAT can be loaded as a module:

[asrini@node061 ~]$  module load blat-v3

[asrini@node061 ~]$  blat
blat - Standalone BLAT v. 35 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.
   Subranges of nib and .2bit files may specified using the syntax:
      /path/file.nib:seqid:start-end
   or
      /path/file.2bit:seqid:start-end
   or
      /path/file.nib:start-end
   With the second form, a sequence id of file:start-end will be used.

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