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.
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/
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
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.