HOMER: Difference between revisions
Jump to navigation
Jump to search
Moskalenko (talk | contribs) No edit summary |
Moskalenko (talk | contribs) m Text replacement - "#uppercase" to "uc" |
||
| Line 33: | Line 33: | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
* HPC_{{ | * HPC_{{uc:{{#var:app}}}}_DIR | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:21, 6 December 2019
Description
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
Required Modules
Serial
- homer
System Variables
- HPC_HOMER_DIR
Additional Information
Specify -preparsedDir <directory> while running findMotifsGenome.pl to store the pre-parsed genome files locally as the data/genomes/*/preparsed/ are not writable by users.
Validation
- Validated 4/5/2018