KentUtils

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Introduction

A myriad of bioinformatics tools from Jim Kent

The tools

addCols           bedGraphToBigWig        bigWigCorrelate   chainStitchId      faCmp          featureBits          hgFindSpec     linesToRa         mafToAxt        paraFetch            pslSort      spacedToTab        validateFiles
ameme             bedIntersect            bigWigInfo        chainSwap          faCount        fetchChromSizes      hgGcPercent    localtime         mafToPsl        paraSync             pslStats     splitFile          validateManifest
autoDtd           bedItemOverlapCount     bigWigMerge       chainToAxt         faFilter       findMotif            hgLoadBed      mafAddIRows       makeTableList   positionalTblCheck   pslSwap      splitFileByColumn  wigCorrelate
autoSql           bedPileUps              bigWigSummary     chainToPsl         faFilterN      gapToLift            hgLoadOut      mafAddQRows       maskOutFa       pslCat               pslToBed     sqlToXml           wigEncode
autoXml           bedRemoveOverlap        bigWigToBedGraph  checkAgpAndFa      faFrag         genePredCheck        hgLoadWiggle   mafCoverage       mktime          pslCDnaFilter        pslToChain   stringify          wigToBigWig
ave               bedRestrictToPositions  bigWigToWig       checkCoverageGaps  faNoise        genePredHisto        hgsql          mafFetch          mrnaToGene      pslCheck             pslToPslx    subChar            wordLine
aveCols           bedSort                 blastToPsl        checkHgFindSpec    faOneRecord    genePredSingleCover  hgsqldump      mafFilter         netChainSubset  pslDropOverlap       pslxToFa     subColumn          xmlCat
axtChain          bedToBigBed             blastXmlToPsl     checkTableCoords   faPolyASizes   genePredToBed        hgTrackDb      mafFrag           netClass        pslFilter            qacAgpLift   tailLines          xmlToSql
axtSort           bedToExons              calc              chopFaLines        faRandomize    genePredToFakePsl    hgWiggle       mafFrags          netFilter       pslHisto             qacToQa      tdbQuery
axtSwap           bedToGenePred           catDir            chromGraphFromBin  faRc           genePredToGtf        htmlCheck      mafGene           netSplit        pslLiftSubrangeBlat  qacToWig     textHistogram
axtToMaf          bedToPsl                catUncomment      chromGraphToBin    faSize         genePredToMafFrames  hubCheck       mafMeFirst        netSyntenic     pslMap               qaToQac      tickToDate
axtToPsl          bedWeedOverlapping      chainAntiRepeat   colTransform       faSomeRecords  gfClient             ixIxx          mafOrder          netToAxt        pslMrnaCover         randomLines  toLower
bedClip           bigBedInfo              chainFilter       countChars         faSplit        gff3ToGenePred       lavToAxt       mafRanges         netToBed        pslPairs             raSqlQuery   toUpper
bedCommonRegions  bigBedNamedItems        chainMergeSort    crTreeIndexBed     fastqToFa      gff3ToPsl            lavToPsl       mafsInRegion      newProg         pslPartition         raToLines    trfBig
bedCoverage       bigBedSummary           chainNet          crTreeSearchBed    faToFastq      gfServer             ldHgGene       mafSpeciesList    nibFrag         pslPretty            raToTab      twoBitDup
bedExtendRanges   bigBedToBed             chainPreNet       dbSnoop            faToTab        gmtime               liftOver       mafSpeciesSubset  nibSize         pslRecalcMatch       rmFaDups     twoBitInfo
bedGeneParts      bigWigAverageOverBed    chainSort         dbTrash            faToTwoBit     gtfToGenePred        liftOverMerge  mafSplit          oligoMatch      pslReps              rowsToCols   twoBitMask
bedGraphPack      bigWigCat               chainSplit        estOrient          faTrans        headRest             liftUp         mafSplitPos       overlapSelect   pslSelect            sizeof       twoBitToFa