============================== 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.
- 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 flyPROMOTERS: yeast, worm, mouse, arabidopsis, zebrafish, rat, human and flyGENOMES: hg19, hg38, mm10, ce11, dm6, rn6, danRer11, tair10, and sacCer3
You can load the modules by:
module load biocontainers
module load hommer/4.11Example 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