This page will detail how to start using the KentUtils on tetonKentUtils is a suite of tools developed at the USCS Genome Browser lab.
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Module:
Latest:
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[]$ module spider kentutils -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- kentutils: kentutils/1.04.0 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- This |
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module can be loaded directly: module load kentutils/1.04.0
Help:
UCSC Genome Bioinformatics Group's suite of biological analysis and web display programs as well as some of Jim Kent's own tools. |
Using:
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[]$ 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:
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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
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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.