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 flyPROMOTERS
: yeast, worm, mouse, arabidopsis, zebrafish, rat, human and flyGENOMES
: 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