HOMMER

Introduction

HOMMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. Details about its usage can be found in HOMMER website.

Versions

  • 4.11

Commands

  • addDataHeader.pl

  • addData.pl

  • addGeneAnnotation.pl

  • addInternalData.pl

  • addOligos.pl

  • adjustPeakFile.pl

  • adjustRedunGroupFile.pl

  • analyzeChIP-Seq.pl

  • analyzeRepeats.pl

  • analyzeRNA.pl

  • annotateInteractions.pl

  • annotatePeaks.pl

  • annotateRelativePosition.pl

  • annotateTranscripts.pl

  • assignGeneWeights.pl

  • assignTSStoGene.pl

  • batchAnnotatePeaksHistogram.pl

  • batchFindMotifsGenome.pl

  • batchFindMotifs.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

  • chopify.pl

  • chopUpBackground.pl

  • chopUpPeakFile.pl

  • cleanUpPeakFile.pl

  • cleanUpSequences.pl

  • cluster2bedgraph.pl

  • cluster2bed.pl

  • combineGO.pl

  • combineHubs.pl

  • compareMotifs.pl

  • condenseBedGraph.pl

  • cons2fasta.pl

  • conservationAverage.pl

  • conservationPerLocus.pl

  • convertCoordinates.pl

  • convertIDs.pl

  • convertOrganismID.pl

  • duplicateCol.pl

  • eland2tags.pl

  • fasta2tab.pl

  • fastq2fasta.pl

  • filterListBy.pl

  • filterTADsAndCPs.pl

  • filterTADsAndLoops.pl

  • findcsRNATSS.pl

  • findGO.pl

  • findGOtxt.pl

  • findHiCCompartments.pl

  • findHiCDomains.pl

  • findHiCInteractionsByChr.pl

  • findKnownMotifs.pl

  • findMotifsGenome.pl

  • findMotifs.pl

  • findRedundantBLAT.pl

  • findTADsAndLoops.pl

  • findTopMotifs.pl

  • flipPC1toMatch.pl

  • freq2group.pl

  • genericConvertIDs.pl

  • GenomeOntology.pl

  • getChrLengths.pl

  • getConservedRegions.pl

  • getDifferentialBedGraph.pl

  • getDifferentialPeaksReplicates.pl

  • getDiffExpression.pl

  • getDistalPeaks.pl

  • getFocalPeaks.pl

  • getGenesInCategory.pl

  • getGWASoverlap.pl

  • getHiCcorrDiff.pl

  • getHomerQCstats.pl

  • getLikelyAdapters.pl

  • getMappingStats.pl

  • getPartOfPromoter.pl

  • getPos.pl

  • getRandomReads.pl

  • getSiteConservation.pl

  • getTopPeaks.pl

  • gff2pos.pl

  • go2cytoscape.pl

  • groupSequences.pl

  • joinFiles.pl

  • loadGenome.pl

  • loadPromoters.pl

  • makeBigBedMotifTrack.pl

  • makeBigWig.pl

  • makeBinaryFile.pl

  • makeHiCWashUfile.pl

  • makeMetaGeneProfile.pl

  • makeMultiWigHub.pl

  • map-fastq.pl

  • merge2Dbed.pl

  • mergeData.pl

  • motif2Jaspar.pl

  • motif2Logo.pl

  • parseGTF.pl

  • pos2bed.pl

  • preparseGenome.pl

  • prepForR.pl

  • profile2seq.pl

  • qseq2fastq.pl

  • randomizeGroupFile.pl

  • randomizeMotifs.pl

  • randRemoveBackground.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

  • selectRepeatBg.pl

  • seq2profile.pl

  • SIMA.pl

  • subtractBedGraphsDirectory.pl

  • subtractBedGraphs.pl

  • tab2fasta.pl

  • tag2bed.pl

  • tag2pos.pl

  • tagDir2bed.pl

  • tagDir2hicFile.pl

  • tagDir2HiCsummary.pl

  • zipHomerResults.pl

Database

Selected database have been downloaded for users.

  • ORGANISMS: yeast, worm, mouse, arabidopsis, zebrafish, rat, human and fly

  • PROMOTERS: yeast, worm, mouse, arabidopsis, zebrafish, rat, human and fly

  • GENOMES: hg19, hg38, mm10, ce11, dm6, rn6, danRer11, tair10, and sacCer3

Module

You can load the modules by:

module load biocontainers
module load hommer/4.11

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 HOMMER on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=hommer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers hommer/4.11

configureHomer.pl -list   ## Check the installed database.
findMotifs.pl mouse_geneid.txt mouse motif_out_mouse
findMotifs.pl geneid.txt human motif_out