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