Overview
KentUtils is a suite of tools developed at the USCS Genome Browser lab.
Manual: To understand how an individual command works, type its name at the command line with no arguments. The resulting message will provide basic details of what the command does as well as some instructions on using it as well as a list of usable options. See the examples above.
Using
Use the module name kentutils to discover versions available and to load the application.
Example
[]$ module load kentutils/1.04.0
[salexan5@tlog1 ~]$ axtChain
axtChain - Chain together axt alignments.
usage:
axtChain [options] -linearGap=loose in.axt tNibDir qNibDir out.chain
Where tNibDir/qNibDir are either directories full of nib files, the name
of a .2bit file, or a single fasta file with additional -faQ or -faT options.
options:
-psl Use psl instead of axt format for input
-faQ The specified qNibDir is a fasta file with multiple sequences for query
-faT The specified tNibDir is a fasta file with multiple sequences for target
NOTE: will not work with gzipped fasta files
-minScore=N Minimum score for chain, default 1000
-details=fileName Output some additional chain details
-scoreScheme=fileName Read the scoring matrix from a blastz-format file
-linearGap=<medium|loose|filename> Specify type of linearGap to use.
*Must* specify this argument to one of these choices.
loose is chicken/human linear gap costs.
medium is mouse/human linear gap costs.
Or specify a piecewise linearGap tab delimited file.
sample linearGap file (loose)
tablesize 11
smallSize 111
position 1 2 3 11 111 2111 12111 32111 72111 152111 252111
qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600
bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000
[salexan5@tlog1 ~]$ chainMergeSort
chainMergeSort - Combine sorted files into larger sorted file
usage:
chainMergeSort file(s)
Output goes to standard output
options:
-saveId - keep the existing chain ids.
-inputList=somefile - somefile contains list of input chain files.
-tempDir=somedir/ - somedir has space for temporary sorting data, default ./
This suite of tools contains over 300 individual commands:
addCols bigBedSummary checkTableCoords fetchChromSizes hgSpeciesRna mafSplitPos pslFilter splitFile ameme bigBedToBed chopFaLines findMotif hgsql mafToAxt pslHisto splitFileByColumn autoDtd bigGenePredToGenePred chromGraphFromBin fixStepToBedGraph.pl hgsqldump mafToBigMaf pslLiftSubrangeBlat sqlToXml autoSql bigHeat chromGraphToBin FOOTER.txt hgTrackDb mafToPsl pslMap strexCalc autoXml bigMafToMaf chromToUcsc gapToLift hgvsToVcf mafToSnpBed pslMapPostChain stringify ave bigPslToPsl clusterGenes genePredCheck hgWiggle makeTableList pslMrnaCover subChar aveCols bigWigAverageOverBed colTransform genePredFilter hicInfo maskOutFa pslPairs subColumn axtChain bigWigCat countChars genePredHisto htmlCheck mktime pslPartition tabQuery axtSort bigWigCluster cpg_lh genePredSingleCover hubCheck mrnaToGene pslPosTarget tailLines axtSwap bigWigCorrelate crTreeIndexBed genePredToBed hubClone netChainSubset pslPretty tdbQuery axtToMaf bigWigInfo crTreeSearchBed genePredToBigGenePred hubPublicCheck netClass pslRc tdbRename axtToPsl bigWigMerge dbSnoop genePredToFakePsl ixIxx netFilter pslRecalcMatch tdbSort bamToPsl bigWigSummary dbTrash genePredToGtf lastz-1.04.00 netSplit pslRemoveFrameShifts textHistogram barChartMaxLimit bigWigToBedGraph endsInLf genePredToMafFrames lastz_D-1.04.00 netSyntenic pslReps tickToDate bedClip bigWigToWig estOrient genePredToProt lavToAxt netToAxt pslScore toLower bedCommonRegions binFromRange expMatrixToBarchartBed gensub2 lavToPsl netToBed pslSelect toUpper bedCoverage blastToPsl faAlign getRna ldHgGene newProg pslSomeRecords trackDbIndexBb bedExtendRanges blastXmlToPsl faCmp getRnaPred liftOver newPythonProg pslSort transMapPslToGenePred bedGeneParts blat faCount gff3ToGenePred liftOverMerge nibFrag pslStats trfBig bedGraphPack calc faFilter gff3ToPsl liftUp nibSize pslSwap twoBitDup bedGraphToBigWig catDir faFilterN gmtime linesToRa oligoMatch pslToBed twoBitInfo bedIntersect catUncomment faFrag gtfToGenePred localtime overlapSelect pslToBigPsl twoBitMask bedItemOverlapCount chainAntiRepeat faNoise headRest mafAddIRows para pslToChain twoBitToFa bedJoinTabOffset chainBridge faOneRecord hgBbiDbLink mafAddQRows paraFetch pslToPslx ucscApiClient bedJoinTabOffset.py chainFilter faPolyASizes hgFakeAgp mafCoverage paraHub pslxToFa udr bedMergeAdjacent chainMergeSort faRandomize hgFindSpec mafFetch paraHubStop qacAgpLift vai.pl bedPartition chainNet faRc hgGcPercent mafFilter paraNode qacToQa validateFiles bedPileUps chainPreNet faSize hgGoldGapGl mafFrag paraNodeStart qacToWig validateManifest bedRemoveOverlap chainSort faSomeRecords hgLoadBed mafFrags paraNodeStatus qaToQac varStepToBedGraph.pl bedRestrictToPositions chainSplit faSplit hgLoadChain mafGene paraNodeStop randomLines webSync bedSort chainStitchId fastqStatsAndSubsample hgLoadGap mafMeFirst parasol raSqlQuery wigCorrelate bedToBigBed chainSwap fastqToFa hgLoadMaf mafNoAlign paraSync raToLines wigEncode bedToExons chainToAxt faToFastq hgLoadMafSummary mafOrder paraTestJob raToTab wigToBigWig bedToGenePred chainToPsl faToTab hgLoadNet mafRanges positionalTblCheck README.txt wordLine bedToPsl chainToPslBasic faToTwoBit hgLoadOut mafsInRegion pslCat rmFaDups xmlCat bedWeedOverlapping checkAgpAndFa faToVcf hgLoadOutJoined mafSpeciesList pslCDnaFilter rowsToCols xmlToSql bigBedInfo checkCoverageGaps faTrans hgLoadSqlTab mafSpeciesSubset pslCheck sizeof bigBedNamedItems checkHgFindSpec featureBits hgLoadWiggle mafSplit pslDropOverlap spacedToTab