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:
