Difference between revisions of "HPC:Homer"
From HPC wiki
(Created page with "=== HOMER === HOMER vv4.6, 3-29-2014 is installed across all HPC nodes. ==== Usage ==== HOMER can be loaded as a module: <pre> [asrini@node061 ~]$ module load homer-v4.6 [...") |
|||
| (3 intermediate revisions by one other user not shown) | |||
| Line 1: | Line 1: | ||
=== HOMER === | === HOMER === | ||
| − | HOMER | + | HOMER v4.6, 3-29-2014 is installed across all HPC nodes. |
==== Usage ==== | ==== Usage ==== | ||
| Line 21: | Line 21: | ||
-seed <file> : seed file | -seed <file> : seed file | ||
-offset <#> : offset of sequence from TSS (-2000) | -offset <#> : offset of sequence from TSS (-2000) | ||
| + | |||
| + | </pre> | ||
| + | |||
| + | Homer was compiled with our version of BLAT so you should also load that module | ||
| + | |||
| + | <pre> | ||
| + | [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. | ||
| + | |||
</pre> | </pre> | ||
=== 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 15:41, 13 August 2019
HOMER
HOMER v4.6, 3-29-2014 is installed across all HPC nodes.
Usage
HOMER can be loaded as a module:
[asrini@node061 ~]$ module load homer-v4.6 [asrini@node061 ~]$ homer homer : Empirical Motif Optimizer usage: ./homer [data] [parameters] -a [action] This program is meant to be called from other programs (i.e. findMotifsGenome.pl), and not used directly Data options: -dna|-prot : Sequence type (-dna) -s <file> : Sequence File -g <file> : Group/Stat File -mer <file> : Mer File -m <file> : PSSM Motif File -o <file> : output file prefix -seed <file> : seed file -offset <#> : offset of sequence from TSS (-2000)
Homer was compiled with our version of BLAT so you should also load that 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.
