Purdue University

homer

HOMER (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 HOMER website.

Link to section 'Versions' of 'homer' Versions

• 4.11

Link to section 'Commands' of 'homer' 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

Link to section 'Database' of 'homer' 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

Link to section 'Module' of 'homer' Module

You can load the modules by:

module load biocontainers
module load homer/4.11

Link to section 'Example job' of 'homer' Example job

To run HOMER on our cluster:

#!/bin/bash
#SBATCH -A myallocation	# Allocation name 
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#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
ml biocontainers homer/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