Difference between revisions of "HPC:BLAT"
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(Created page with "=== BLAT === UCSC's BLAT is installed across all HPC nodes. ==== Usage ==== BLAT can be loaded as a module: <pre> [asrini@node061 ~]$ module load blat-v3 [asrini@node061 ...") |
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=== Other Pages === | === Other Pages === | ||
| + | ---- | ||
| + | <div class="mw-collapsible mw-collapsed"> | ||
| + | *[[HPC:FAQ|HPC FAQ ]] | ||
| + | *[[HPC:Login|Connecting to the PMACS cluster]] | ||
| + | *[[HPC:User_Guide|User Guide]] | ||
*[[HPC:Software|Available Software]] | *[[HPC:Software|Available Software]] | ||
| − | *[[HPC: | + | *[[HPC:Archive System|PMACS Archive System]] |
| − | + | </div> | |
| − | |||
Latest revision as of 15:18, 13 August 2019
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.
