Homer

Introduction

HOMER is a suite of tools for Motif Discovery and next-gen sequencing analysis.

For more information, please check:
Home page: http://homer.ucsd.edu/homer/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

4.11

BELL

4.11

GAUTSCHI

4.11

NEGISHI

4.11

SCHOLAR

4.11

Commands

  • GenomeOntology.pl

  • HomerConfig.pm

  • HomerSVGLogo.pm

  • SIMA.pl

  • Statistics.pm

  • addData.pl

  • addDataHeader.pl

  • addGeneAnnotation.pl

  • addInternalData.pl

  • addOligos.pl

  • adjustPeakFile.pl

  • adjustRedunGroupFile.pl

  • analyzeChIP-Seq.pl

  • analyzeHiC

  • analyzeRNA.pl

  • analyzeRepeats.pl

  • annotateInteractions.pl

  • annotatePeaks.pl

  • annotateRelativePosition.pl

  • annotateTranscripts.pl

  • assignGeneWeights.pl

  • assignGenomeAnnotation

  • assignTSStoGene.pl

  • batchAnnotatePeaksHistogram.pl

  • batchFindMotifs.pl

  • batchFindMotifsGenome.pl

  • batchMakeHiCMatrix.pl

  • batchMakeMultiWigHub.pl

  • batchMakeTagDirectory.pl

  • batchParallel.pl

  • bed2DtoUCSCbed.pl

  • bed2pos.pl

  • bed2tag.pl

  • blat2gtf.pl

  • bridgeResult2Cytoscape.pl

  • changeNewLine.pl

  • checkPeakFile.pl

  • checkTagBias.pl

  • chopUpBackground.pl

  • chopUpPeakFile.pl

  • chopify.pl

  • cleanUpPeakFile.pl

  • cleanUpSequences.pl

  • cluster2bed.pl

  • cluster2bedgraph.pl

  • combineGO.pl

  • combineHubs.pl

  • compareMotifs.pl

  • condenseBedGraph.pl

  • cons2fasta.pl

  • conservationAverage.pl

  • conservationPerLocus.pl

  • convertCoordinates.pl

  • convertIDs.pl

  • convertOrganismID.pl

  • createIGVhtml.pl

  • duplicateCol.pl

  • eland2tags.pl

  • fasta2tab.pl

  • fastq2fasta.pl

  • filterListBy.pl

  • filterTADsAndCPs.pl

  • filterTADsAndLoops.pl

  • filterTagDirectory.pl

  • findGO.pl

  • findGOtxt.pl

  • findHiCCompartments.pl

  • findHiCDomains.pl

  • findHiCInteractionsByChr.pl

  • findKnownMotifs.pl

  • findMotifs.pl

  • findMotifsGenome.pl

  • findPeaks

  • findRedundantBLAT.pl

  • findTADsAndLoops.pl

  • findTADsAndLoopsFromRelMatrix

  • findTopMotifs.pl

  • findcsRNATSS.pl

  • flipPC1toMatch.pl

  • freq2group.pl

  • genericConvertIDs.pl

  • genomeOntology

  • getChrLengths.pl

  • getConservedRegions.pl

  • getDiffExpression.pl

  • getDifferentialBedGraph.pl

  • getDifferentialPeaks

  • getDifferentialPeaksReplicates.pl

  • getDistalPeaks.pl

  • getFocalPeaks.pl

  • getGWASoverlap.pl

  • getGenesInCategory.pl

  • getGenomeTilingPeaks

  • getHiCcorrDiff.pl

  • getHomerQCstats.pl

  • getLikelyAdapters.pl

  • getMappableRegions

  • getMappingStats.pl

  • getPartOfPromoter.pl

  • getPeakTags

  • getPos.pl

  • getRandomReads.pl

  • getSiteConservation.pl

  • getTopPeaks.pl

  • gff2pos.pl

  • go2cytoscape.pl

  • groupSequences.pl

  • homer

  • homer2

  • homerTools

  • joinFiles.pl

  • loadGenome.pl

  • loadPromoters.pl

  • makeBigBedMotifTrack.pl

  • makeBigWig.pl

  • makeBinaryFile.pl

  • makeHiCWashUfile.pl

  • makeMetaGeneProfile.pl

  • makeMultiWigHub.pl

  • makeTagDirectory

  • makeUCSCfile

  • map-fastq.pl

  • merge2Dbed.pl

  • mergeData.pl

  • mergePeaks

  • motif2Jaspar.pl

  • motif2Logo.pl

  • old

  • parseGTF.pl

  • pos2bed.pl

  • prepForR.pl

  • preparseGenome.pl

  • profile2seq.pl

  • qseq2fastq.pl

  • randRemoveBackground.pl

  • randomizeGroupFile.pl

  • randomizeMotifs.pl

  • removeAccVersion.pl

  • removeBadSeq.pl

  • removeOutOfBoundsReads.pl

  • removePoorSeq.pl

  • removeRedundantPeaks.pl

  • renamePeaks.pl

  • resizePosFile.pl

  • revoppMotif.pl

  • rotateHiCmatrix.pl

  • runHiCpca.pl

  • sam2spliceJunc.pl

  • scanMotifGenomeWide.pl

  • scrambleFasta.pl

  • configureHomer.pl

Module

You can load the modules by:

module load biocontainers
module load homer

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run homer on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer

# Your homer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer

# Your homer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer

# Your homer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer

# Your homer workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer

# Your homer workflow...