| The CSF2 has been replaced by the CSF3 - please use that system! This documentation may be out of date. Please read the CSF3 documentation instead. To display this old CSF2 page click here. |
HOMER
Overview
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
Version 4.8.2 and 4.10.1 are installed on the CSF:
Version 4.10.1:
- The base software is installed, datasets mouse-o, mouse-p, mm8, hg19, hg38 have been included.
- Weblogo is no longer required so is NOT installed.
- BLAT has NOT been included.
Version 4.8.2:
- Only the base software is installed, NO datasets / sequences etc have been included.
- Weblogo has been included for
seqlogo. - BLAT has NOT been included.
Restrictions on use
HOMER is free software and available to all users of the system. Please ensure you cite your usage in any results and publications as per the HOMER website.
Set up procedure
To access the software you must first load the modulefile:
module load apps/binapps/homer/4.10.1 module load apps/binapps/homer/4.8.2
Running the application
Please do not run HOMER on the login node. Jobs should be submitted to the compute nodes via batch.
You may run the tool on the login node with the -help flag to see the command-line flags accepted by the tool.
Note that if the HOMER tool you run generates parsed files (e.g., ) then you should inform the tool where to write those files. By default it may try to write them in the centrall installation area to which you do not have write access. Check whether your tool accepts the flag:
-preparsedDir path/to/local/folder
which allows you to specify the name of a local folder (e.g., ~/scratch/homer_data).
Serial batch job submission
Make sure you have the serial version of the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings # Example using the findMotifsGenome.pl tool: findMotifsGenome.pl peaks.txt mm8r peakAnalysis -size 200 -len 8 -preparsedDir ~/scratch/my_homer_data
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.