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UCSC Executables

The UCSC Genome Browser is maintained using a variety of executables that perform functions ranging from sequence analysis and format conversion, to basic number crunching and statistics, to complex database generation and manipulation.

These executables have been compiled and made available on the Helix Systems.

How to use

The easiest way is to load the ucsc environment module:

$ module load ucsc

The module load statement can be placed in your startup files for permanency.

Then, just call the executable of choice on the commandline:

$ faSplit byname scaffolds.fa outRoot/

List of current executables

aarToAxt			edwReallyRemoveFiles		hgNibSeq			pslScore
addAveMedScoreToPsls		edwReplicatedPeaks		hgPar				pslSelect
addCols				edwRetryJob			hgPepPred			pslSimp
affyPairsToSample		edwRsyncEdwUser			hgPhMouse			pslSort
agpAllToFaFile			edwRunDaemon			hgProtIdToGenePred		pslSortAcc
agpCloneCheck			edwRunOnIds			hgRatioMicroarray		pslSplitOnTarget
agpCloneList			edwSamPairedEndStats		hgRenameSplitTable		pslStats
agpToFa				edwSamRepeatAnalysis		hgRnaGenes			pslSwap
agpToGl				edwSolexaToSangerFastq		hgSanger20			pslToBed
agxToBed			edwSubmit			hgSanger22			pslToChain
agxToIntronBeds			eisenInput			hgSelect			pslToPslx
agxToTxg			emblMatrixToMotif		hgSgdGff3			pslToXa
allenCollectSeq			embossToPsl			hgSgdGfp			pslUniq
altAnalysis			endsInLf			hgSgdPep			pslUnpile
altPaths			estLibStats			hgSoftberryHom			pslxToFa
altSplice			estOrient			hgSoftPromoter			qacAgpLift
altSummary			exonerateGffDoctor		hgSpeciesRna			qacToQa
aNotB				expToRna			hgsql				qacToWig
apacheMonitor			faAlign				hgsqladmin			qaToQac
assessLibs			faCmp				hgsqldump			randomLines
autoDtd				faCount				hgsqldumpLocal			raSqlQuery
autoSql				faFilter			hgsqlimport			raToCds
autoXml				faFilterN			hgsqlLocal			raToLines
ave				faFlyBaseToUcsc			hgsqlSwapTables			raToTab
aveCols				faFrag				hgsqlTableDate			refreshNamedSessionCustomTracks
averagExp			faGapLocs			hgStanfordMicroarray		refSeqGet
averageZoomLevels		faGapSizes			hgStsAlias			regionPicker
avgTranscriptomeExps		fakeFinContigs			hgStsMarkers			relPairs
axtAndBed			fakeOut				hgSuperfam			reviewIndexes
axtBest				faNcbiToUcsc			hgTablesTest			reviewSanity
axtCalcMatrix			faNoise				hgTomRough			rikenBestInCluster
axtChain			faOneRecord			hgTpf				rmFaDups
axtDropOverlap			faPolyASizes			hgTraceInfo			rnaFoldBig
axtDropSelf			faRandomize			hgTrackDb			rowsToCols
axtFilter			faRc				hgTracksRandom			safePush
axtForEst			faSimplify			hgWaba				samHit
axtIndex			faSize				hgWiggle			sanger22gtf
axtPretty			faSomeRecords			hgWormLinks			scaffoldFaToAgp
axtQueryCount			faSplit				hgYeastRegCode			scaleSampleFiles
axtRecipBest			fastqToFa			hprdP2p				scanRa
axtRescore			faToFastq			htmlCheck			scrambleFa
axtSort				faToNib				htmlPics			semiNorm
axtSplitByTarget		faToTab				hubCheck			seqCheck
axtSwap				faToTwoBit			hubPublicCheck			sequenceForBed
axtToBed			faTrans				intronEnds			sim4big
axtToChain			faTrimPolyA			iriToControlTable		simpleChain
axtToMaf			faTrimRead			iriToDnaMotif			sizeof
axtToPsl			featureBits			isPcr				snpException
bedClip				ffaToFa				jkUniq				snpMaskAddInsertions
bedCommonRegions		findMotif			joinableFields			snpMaskCutDeletions
bedCons				findStanAlignments		joinerCheck			snpMaskSingle
bedCoverage			fishClones			knownToHprd			snpNcbiToUcsc
bedDown				fixCr				knownToVisiGene			snpValid
bedExtendRanges			fixHarbisonMotifs		knownVsBlat			spacedToTab
bedGeneParts			fqToQa				kvsSummary			spideyToPsl
bedGraphPack			fqToQac				lavToAxt			splitFa
bedGraphToBigWig		fragPart			lavToPsl			splitFaIntoContigs
bedInGraph			gapSplit			ldHgGene			splitFile
bedIntersect			gapToLift			lfsOverlap			splitFileByColumn
bedItemOverlapCount		gbGetEntries			libScan				splitSim
bedOrBlocks			gbOneAcc			liftAcross			sqlToXml
bedPileUps			gbSeqCheck			liftAgp				stageMultiz
bedRemoveOverlap		gbToFaRa			liftFrags			stanToBedAndExpRecs
bedRestrictToPositions		gcForBed			liftOver			stringify
bedSort				genePredCheck			liftOverMerge			subChar
bedSplitOnChrom			genePredHisto			liftPromoHits			subColumn
bedToBigBed			genePredSingleCover		liftUp				subs
bedToExons			genePredToBed			lineCount			subsetAxt
bedToFrames			genePredToFakePsl		linesToRa			subsetTraces
bedToGenePred			genePredToGtf			localtime			tableSum
bedToPsl			genePredToMafFrames		mafAddIRows			tailLines
bedToTxEdges			genePredToPsl			mafAddQRows			tdbQuery
bedUp				geoMirrorNode			mafCoverage			testSearch
bedWeedOverlapping		getChroms			mafFetch			textHist2
bigBedInfo			getFeatDna			mafFilter			textHistogram
bigBedNamedItems		getRna				mafFrag				tfbsConsLoc
bigBedSummary			getRnaPred			mafFrags			tfbsConsSort
bigBedToBed			gfClient			mafGene				tickToDate
bigWigAverageOverBed		gff3ToGenePred			mafMeFirst			timePosTable
bigWigCat			gff3ToPsl			mafOrder			toDev64
bigWigCorrelate			gffPeek				mafRanges			toLower
bigWigInfo			gfPcr				mafsInRegion			toUpper
bigWigMerge			gfServer			mafSpeciesList			trackDbPatch
bigWigSummary			git-reports			mafSpeciesSubset		trackDbRaFormat
bigWigToBedGraph		gmtime				mafSplit			trackOverlap
bigWigToWig			gpcrParser			mafSplitPos			trfBig
blastToPsl			gpStats				mafToAxt			twinOrf
blastXmlToPsl			gpToGtf				mafToPsl			twinOrf2
blat				groupSamples			mafToSnpBed			twinOrf3
blatz				gsBig				makeTableDescriptions		twinOrfStats
blatzClient			gtfToGenePred			makeTableList			twinOrfStats2
blatzServer			hapmapPhaseIIISummary		makeTrackIndex			twinOrfStats3
borfBig				headRest			maskOutFa			twoBitDup
calc				hgAddLiftOverChain		maxTranscriptomeExps		twoBitInfo
calcGap				hgAvidShortBed			mdbPrint			twoBitMask
catDir				hgBbiDbLink			mdbUpdate			twoBitToFa
catUncomment			hgBioCyc			mdToNcbiLift			txAbFragFind
ccCp				hgCeOrfToGene			mgcFastaForBed			txBedToGraph
chainAntiRepeat			hgCGAP				mktime				txCdsBadBed
chainDbToFile			hgChroms			motifLogo			txCdsCluster
chainFilter			hgClonePos			motifSig			txCdsEvFromBed
chainMergeSort			hgClusterGenes			mousePoster			txCdsEvFromBorf
chainNet			hgCountAlign			mrnaToGene			txCdsEvFromProtein
chainPreNet			hgCtgPos			mysqlSecurityCheck		txCdsEvFromRna
chainSort			hgDeleteChrom			netChainSubset			txCdsGoodBed
chainSplit			hgDropSplitTable		netClass			txCdsOrfInfo
chainStats			hgEmblProtLinks			netFilter			txCdsOrtho
chainStitchId			hgExonerate			netSplit			txCdsPick
chainSwap			hgExpDistance			netStats			txCdsPredict
chainToAxt			hgExperiment			netSyntenic			txCdsRaExceptions
chainToPsl			hgExtFileCheck			netToAxt			txCdsRefBestEvOnly
checkableBorf			hgFakeAgp			netToBed			txCdsRepick
checkAgpAndFa			hgFiberglass			netToBedWithId			txCdsSuspect
checkCardinality		hgFindSpec			newProg				txCdsSvmInput
checkChain			hgFlyBase			nibbImageProbes			txCdsToGene
checkCoverageGaps		hgGcPercent			nibbNameFix			txCdsWeed
checkHgFindSpec			hgGeneBands			nibbParseImageDir		txgAddEvidence
checkSgdSync			hgGenericMicroarray		nibbPrepImages			txgAnalyze
checkTableCoords		hgGetAnn			nibFrag				txGeneAccession
chopFaLines			hgGnfMicroarray			nibSize				txGeneAlias
chromGraphFromBin		hgGoAssociation			normalizeSampleFile		txGeneAltProt
chromGraphToBin			hgGoldGapGl			nt4Frag				txGeneCanonical
clusterGenes			hgGtex				oligoMatch			txGeneCdsMap
clusterPsl			hgJaxQtl			orf				txGeneColor
clusterRna			hgKegg				orfStats			txGeneExplainUpdate1
colTransform			hgKegg2				orthoEvaluate			txGeneFromBed
consForBed			hgKegg3				orthologBySynteny		txGeneProtAndRna
convolve			hgKgGetText			orthoMap			txGeneSeparateNoncoding
countChars			hgKgMrna			orthoPickIntron			txGeneXref
countNib			hgKnownGeneList			orthoSplice			txgGoodEdges
createSageSummary		hgKnownMore			overlapSelect			txgToAgx
crTreeIndexBed			hgKnownToSuper			paraFetch			txgToXml
crTreeSearchBed			hgLoadBed			paraSync			txgTrim
ctgFaToFa			hgLoadBlastTab			patCount			txInfoAssemble
ctgToChromFa			hgLoadChain			pepPredToFa			txOrtho
dbFindFieldsWith		hgLoadChromGraph		phToPsl				txPslFilter
dbSnoop				hgLoadEranModules		polyInfo			txPslToBed
dbTrash				hgLoadGap			positionalTblCheck		txReadRa
detab				hgLoadGenePred			promoSeqFromCluster		txWalk
dnaMotifFind			hgLoadItemAttr			pslCat				udcCleanup
dumpNib				hgLoadMaf			pslCDnaFilter			undupFa
edwAddAssembly			hgLoadMafFrames			pslCheck			uniqSize
edwAddQaContamTarget		hgLoadMafSummary		pslCoverage			updateStsInfo
edwAddQaEnrichTarget		hgLoadNet			pslDiff				upper
edwAddSubscriber		hgLoadNetDist			pslDropOverlap			utrFa
edwBamFilter			hgLoadOut			pslFilter			validateFiles
edwBamRemoveChrom		hgLoadOutJoined			pslFilterPrimers		validateManifest
edwBamStats			hgLoadPsl			pslGlue				vegaBuildInfo
edwChangeFormat			hgLoadRnaFold			pslHisto			venn
edwComparePeaks			hgLoadSample			pslHitPercent			verticalSplitSqlTable
edwCorrectFileTags		hgLoadSeq			pslIntronsOnly			weedLines
edwCreateUser			hgLoadSqlTab			pslLiftSubrangeBlat		whyConserved
edwFakeManifestFromSubmit	hgLoadWiggle			pslMap				wigBedToStep
edwJob				hgLsSnpPdbLoad			pslMrnaCover			wigCorrelate
edwMakeContaminationQa		hgMapMicroarray			pslPairs			wigEncode
edwMakeEnrichments		hgMapToGene			pslPartition			wigTestMaker
edwMakePairedEndQa		hgMapViaSwissProt		pslPosTarget			wigToBigWig
edwMakeRepeatQa			hgMedianMicroarray		pslPretty			wordLine
edwMakeReplicateQa		hgMrnaRefseq			pslQuickFilter			xmlCat
edwMakeValidFile		hgNearTest			pslRecalcMatch			xmlToSql
edwQaEvaluate			hgNetDist			pslReps

Documentation

For most of the executables, issuing the command without any arguments will give a brief description of the executable.

For example:

$ twoBitToFa 
twoBitToFa - Convert all or part of .2bit file to fasta
usage:
   twoBitToFa input.2bit output.fa
options:
   -seq=name - restrict this to just one sequence
   -start=X  - start at given position in sequence (zero-based)
   -end=X - end at given position in sequence (non-inclusive)
   -seqList=file - file containing list of the desired sequence names 
                    in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
                    where coordinates are half-open zero-based, i.e. [start,end)
   -noMask - convert sequence to all upper case
   -bpt=index.bpt - use bpt index instead of built in one
   -bed=input.bed - grab sequences specified by input.bed. Will exclude introns
   -bedPos        - with -bed, to use chrom:start-end as the fasta ID in output.fa

Sequence and range may also be specified as part of the input
file name using the syntax:
      /path/input.2bit:name
   or
      /path/input.2bit:name
   or
      /path/input.2bit:name:start-end

Many of the executables are poorly documented. For further help, you can submit questions to the main UCSC discussion list. See http://genome.ucsc.edu/contacts.html.