ucsc_genome_toolkit
UCSC Executables is 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 downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ and made available on RCAC clusters.
Link to section 'Versions' of 'ucsc_genome_toolkit' Versions
- 369
Link to section 'Commands' of 'ucsc_genome_toolkit' Commands
- addCols
- ameme
- autoDtd
- autoSql
- autoXml
- ave
- aveCols
- axtChain
- axtSort
- axtSwap
- axtToMaf
- axtToPsl
- bamToPsl
- barChartMaxLimit
- bedClip
- bedCommonRegions
- bedCoverage
- bedExtendRanges
- bedGeneParts
- bedGraphPack
- bedGraphToBigWig
- bedIntersect
- bedItemOverlapCount
- bedJoinTabOffset
- bedJoinTabOffset.py
- bedMergeAdjacent
- bedPartition
- bedPileUps
- bedRemoveOverlap
- bedRestrictToPositions
- bedSingleCover.pl
- bedSort
- bedToBigBed
- bedToExons
- bedToGenePred
- bedToPsl
- bedWeedOverlapping
- bigBedInfo
- bigBedNamedItems
- bigBedSummary
- bigBedToBed
- bigGenePredToGenePred
- bigHeat
- bigMafToMaf
- bigPslToPsl
- bigWigAverageOverBed
- bigWigCat
- bigWigCluster
- bigWigCorrelate
- bigWigInfo
- bigWigMerge
- bigWigSummary
- bigWigToBedGraph
- bigWigToWig
- binFromRange
- blastToPsl
- blastXmlToPsl
- blat
- calc
- catDir
- catUncomment
- chainAntiRepeat
- chainBridge
- chainCleaner
- chainFilter
- chainMergeSort
- chainNet
- chainPreNet
- chainScore
- chainSort
- chainSplit
- chainStitchId
- chainSwap
- chainToAxt
- chainToPsl
- chainToPslBasic
- checkAgpAndFa
- checkCoverageGaps
- checkHgFindSpec
- checkTableCoords
- chopFaLines
- chromGraphFromBin
- chromGraphToBin
- chromToUcsc
- clusterGenes
- clusterMatrixToBarChartBed
- colTransform
- countChars
- cpg_lh
- crTreeIndexBed
- crTreeSearchBed
- dbSnoop
- dbTrash
- endsInLf
- estOrient
- expMatrixToBarchartBed
- faAlign
- faCmp
- faCount
- faFilter
- faFilterN
- faFrag
- faNoise
- faOneRecord
- faPolyASizes
- faRandomize
- faRc
- faSize
- faSomeRecords
- faSplit
- faToFastq
- faToTab
- faToTwoBit
- faToVcf
- faTrans
- fastqStatsAndSubsample
- fastqToFa
- featureBits
- fetchChromSizes
- findMotif
- fixStepToBedGraph.pl
- gapToLift
- genePredCheck
- genePredFilter
- genePredHisto
- genePredSingleCover
- genePredToBed
- genePredToBigGenePred
- genePredToFakePsl
- genePredToGtf
- genePredToMafFrames
- genePredToProt
- gensub2
- getRna
- getRnaPred
- gff3ToGenePred
- gff3ToPsl
- gmtime
- gtfToGenePred
- headRest
- hgBbiDbLink
- hgFakeAgp
- hgFindSpec
- hgGcPercent
- hgGoldGapGl
- hgLoadBed
- hgLoadChain
- hgLoadGap
- hgLoadMaf
- hgLoadMafSummary
- hgLoadNet
- hgLoadOut
- hgLoadOutJoined
- hgLoadSqlTab
- hgLoadWiggle
- hgSpeciesRna
- hgTrackDb
- hgWiggle
- hgsql
- hgsqldump
- hgvsToVcf
- hicInfo
- htmlCheck
- hubCheck
- hubClone
- hubPublicCheck
- ixIxx
- lastz-1.04.00
- lastz_D-1.04.00
- lavToAxt
- lavToPsl
- ldHgGene
- liftOver
- liftOverMerge
- liftUp
- linesToRa
- localtime
- mafAddIRows
- mafAddQRows
- mafCoverage
- mafFetch
- mafFilter
- mafFrag
- mafFrags
- mafGene
- mafMeFirst
- mafNoAlign
- mafOrder
- mafRanges
- mafSpeciesList
- mafSpeciesSubset
- mafSplit
- mafSplitPos
- mafToAxt
- mafToBigMaf
- mafToPsl
- mafToSnpBed
- mafsInRegion
- makeTableList
- maskOutFa
- matrixClusterColumns
- matrixMarketToTsv
- matrixNormalize
- mktime
- mrnaToGene
- netChainSubset
- netClass
- netFilter
- netSplit
- netSyntenic
- netToAxt
- netToBed
- newProg
- newPythonProg
- nibFrag
- nibSize
- oligoMatch
- overlapSelect
- para
- paraFetch
- paraHub
- paraHubStop
- paraNode
- paraNodeStart
- paraNodeStatus
- paraNodeStop
- paraSync
- paraTestJob
- parasol
- positionalTblCheck
- pslCDnaFilter
- pslCat
- pslCheck
- pslDropOverlap
- pslFilter
- pslHisto
- pslLiftSubrangeBlat
- pslMap
- pslMapPostChain
- pslMrnaCover
- pslPairs
- pslPartition
- pslPosTarget
- pslPretty
- pslRc
- pslRecalcMatch
- pslRemoveFrameShifts
- pslReps
- pslScore
- pslSelect
- pslSomeRecords
- pslSort
- pslSortAcc
- pslStats
- pslSwap
- pslToBed
- pslToBigPsl
- pslToChain
- pslToPslx
- pslxToFa
- qaToQac
- qacAgpLift
- qacToQa
- qacToWig
- raSqlQuery
- raToLines
- raToTab
- randomLines
- rmFaDups
- rowsToCols
- sizeof
- spacedToTab
- splitFile
- splitFileByColumn
- sqlToXml
- strexCalc
- stringify
- subChar
- subColumn
- tabQuery
- tailLines
- tdbQuery
- tdbRename
- tdbSort
- textHistogram
- tickToDate
- toLower
- toUpper
- trackDbIndexBb
- transMapPslToGenePred
- trfBig
- twoBitDup
- twoBitInfo
- twoBitMask
- twoBitToFa
- ucscApiClient
- udr
- vai.pl
- validateFiles
- validateManifest
- varStepToBedGraph.pl
- webSync
- wigCorrelate
- wigEncode
- wigToBigWig
- wordLine
- xmlCat
- xmlToSql
Link to section 'Module' of 'ucsc_genome_toolkit' Module
You can load the modules by:
module load biocontainers
module load ucsc_genome_toolkit/369
Link to section 'Example job' of 'ucsc_genome_toolkit' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run UCSC executables on our our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=UCSC
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ucsc_genome_toolkit/369
blat genome.fasta input.fasta blat.out
fastqToFa input.fastq output.fasta