Homer

Introduction

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

Versions

• 4.11

Commands

• addDataHeader.pl

• addData.pl

• addGeneAnnotation.pl

• addInternalData.pl

• addOligos.pl

• adjustPeakFile.pl

• adjustRedunGroupFile.pl

• analyzeChIP-Seq.pl

• analyzeHiC

• analyzeRepeats.pl

• analyzeRNA.pl

• annotateInteractions.pl

• annotatePeaks.pl

• annotateRelativePosition.pl

• annotateTranscripts.pl

• assignGeneWeights.pl

• assignGenomeAnnotation

• 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

• configureHomer.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

• findcsRNATSS.pl

• findGO.pl

• findGOtxt.pl

• findHiCCompartments.pl

• findHiCDomains.pl

• findHiCInteractionsByChr.pl

• findKnownMotifs.pl

• findMotifsGenome.pl

• findMotifs.pl

• findPeaks

• findRedundantBLAT.pl

• findTADsAndLoopsFromRelMatrix

• findTADsAndLoops.pl

• findTopMotifs.pl

• flipPC1toMatch.pl

• freq2group.pl

• genericConvertIDs.pl

• genomeOntology

• GenomeOntology.pl

• getChrLengths.pl

• getConservedRegions.pl

• getDifferentialBedGraph.pl

• getDifferentialPeaks

• getDifferentialPeaksReplicates.pl

• getDiffExpression.pl

• getDistalPeaks.pl

• getFocalPeaks.pl

• getGenesInCategory.pl

• getGenomeTilingPeaks

• getGWASoverlap.pl

• 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

• HomerConfig.pm

• HomerSVGLogo.pm

• 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

• 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

• SIMA.pl

• Statistics.pm

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=homer       # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load homer/XXXX ### Latest version is recommended.