Difference between revisions of "HPC:Homer"

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=== HOMER ===
 
=== HOMER ===
HOMER vv4.6, 3-29-2014 is installed across all HPC nodes.
+
HOMER v4.6, 3-29-2014 is installed across all HPC nodes.
  
 
==== Usage ====
 
==== Usage ====
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-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:User_Guide|User Guide]]
+
*[[HPC:Archive System|PMACS Archive System]]
*[[HPC:Main_Page|HPC Main Page]]
+
</div>
*[[HPC:Login|Connecting to the PMACS cluster]]
 

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.


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