Homer2

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

5.1

BELL

5.1

GAUTSCHI

5.1

NEGISHI

5.1

Commands

  • configureHomer.pl

  • GenomeOntology.pl

  • HomerConfig.pm

  • HomerSVGLogo.pm

  • HomerSeqBias.pm

  • SIMA.pl

  • Statistics.pm

  • addData.pl

  • addDataHeader.pl

  • addGeneAnnotation.pl

  • addInternalData.pl

  • addOligos.pl

  • adjustPeakFile.pl

  • adjustPvalueMatrix.pl

  • adjustRedunGroupFile.pl

  • analyzeChIP-Seq.pl

  • analyzeClusters.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

  • calcScore.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

  • createHomer2EnrichmentTable.pl

  • createIGVhtml.pl

  • createScoredFasta.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

  • findcsRNATSR.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

  • getTSSfromReads.pl

  • getTopPeaks.pl

  • gff2pos.pl

  • go2cytoscape.pl

  • groupSequences.pl

  • homer

  • homer2

  • homer2jaspar.pl

  • 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

  • pacifierHomer2.pl

  • parseGTF.pl

  • pos2bed.pl

  • powerSpec.pl

  • prepForR.pl

  • preparseGenome.pl

  • profile2seq.pl

  • qseq2fastq.pl

  • randRemoveBackground.pl

  • randomizeGroupFile.pl

  • randomizeMotif.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

  • script-findAllTSS.pl

  • selectRepeatBg.pl

  • seq2profile.pl

  • subtractBedGraphs.pl

  • subtractBedGraphsDirectory.pl

  • tab2fasta.pl

  • tag2bed.pl

  • tag2pos.pl

  • tagDir2HiCsummary.pl

  • tagDir2bed.pl

  • tagDir2hicFile.pl

  • zipHomerResults.pl

Module

You can load the modules by:

module load biocontainers
module load homer2

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 homer2 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=homer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer2

# Your homer2 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=homer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer2

# Your homer2 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=homer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer2

# Your homer2 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=homer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer2

# Your homer2 workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=homer2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers homer2

# Your homer2 workflow...