Biowulf High Performance Computing at the NIH
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

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

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.