HPC:Homer

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.

Other Pages

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• HPC FAQ
• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System