Kentutils

Introduction

Kentutils: UCSC command line bioinformatic utilities.

For more information, please check:

Docker hub: https://hub.docker.com/r/genomicpariscentre/kentutils

Home page: https://github.com/ENCODE-DCC/kentUtils

Versions

• 302.1.0

Commands

• addCols

• ameme

• autoDtd

• autoSql

• autoXml

• ave

• aveCols

• axtChain

• axtSort

• axtSwap

• axtToMaf

• axtToPsl

• bedClip

• bedCommonRegions

• bedCoverage

• bedExtendRanges

• bedGeneParts

• bedGraphPack

• bedGraphToBigWig

• bedIntersect

• bedItemOverlapCount

• bedPileUps

• bedRemoveOverlap

• bedRestrictToPositions

• bedSort

• bedToBigBed

• bedToExons

• bedToGenePred

• bedToPsl

• bedWeedOverlapping

• bigBedInfo

• bigBedNamedItems

• bigBedSummary

• bigBedToBed

• bigWigAverageOverBed

• bigWigCat

• bigWigCorrelate

• bigWigInfo

• bigWigMerge

• bigWigSummary

• bigWigToBedGraph

• bigWigToWig

• blastToPsl

• blastXmlToPsl

• calc

• catDir

• catUncomment

• chainAntiRepeat

• chainFilter

• chainMergeSort

• chainNet

• chainPreNet

• chainSort

• chainSplit

• chainStitchId

• chainSwap

• chainToAxt

• chainToPsl

• checkAgpAndFa

• checkCoverageGaps

• checkHgFindSpec

• checkTableCoords

• chopFaLines

• chromGraphFromBin

• chromGraphToBin

• colTransform

• countChars

• crTreeIndexBed

• crTreeSearchBed

• dbSnoop

• dbTrash

• estOrient

• faCmp

• faCount

• faFilter

• faFilterN

• faFrag

• faNoise

• faOneRecord

• faPolyASizes

• faRandomize

• faRc

• faSize

• faSomeRecords

• faSplit

• faToFastq

• faToTab

• faToTwoBit

• faTrans

• fastqToFa

• featureBits

• fetchChromSizes

• findMotif

• gapToLift

• genePredCheck

• genePredHisto

• genePredSingleCover

• genePredToBed

• genePredToFakePsl

• genePredToGtf

• genePredToMafFrames

• gfClient

• gfServer

• gff3ToGenePred

• gff3ToPsl

• gmtime

• gtfToGenePred

• headRest

• hgFindSpec

• hgGcPercent

• hgLoadBed

• hgLoadOut

• hgLoadWiggle

• hgTrackDb

• hgWiggle

• hgsql

• hgsqldump

• htmlCheck

• hubCheck

• ixIxx

• lavToAxt

• lavToPsl

• ldHgGene

• liftOver

• liftOverMerge

• liftUp

• linesToRa

• linux.x86_64

• localtime

• mafAddIRows

• mafAddQRows

• mafCoverage

• mafFetch

• mafFilter

• mafFrag

• mafFrags

• mafGene

• mafMeFirst

• mafOrder

• mafRanges

• mafSpeciesList

• mafSpeciesSubset

• mafSplit

• mafSplitPos

• mafToAxt

• mafToPsl

• mafsInRegion

• makeTableList

• maskOutFa

• mktime

• mrnaToGene

• netChainSubset

• netClass

• netFilter

• netSplit

• netSyntenic

• netToAxt

• netToBed

• newProg

• nibFrag

• nibSize

• oligoMatch

• overlapSelect

• paraFetch

• paraSync

• positionalTblCheck

• pslCDnaFilter

• pslCat

• pslCheck

• pslDropOverlap

• pslFilter

• pslHisto

• pslLiftSubrangeBlat

• pslMap

• pslMrnaCover

• pslPairs

• pslPartition

• pslPretty

• pslRecalcMatch

• pslReps

• pslSelect

• pslSort

• pslStats

• pslSwap

• pslToBed

• pslToChain

• pslToPslx

• pslxToFa

• qaToQac

• qacAgpLift

• qacToQa

• qacToWig

• raSqlQuery

• raToLines

• raToTab

• randomLines

• rmFaDups

• rowsToCols

• sizeof

• spacedToTab

• splitFile

• splitFileByColumn

• sqlToXml

• stringify

• subChar

• subColumn

• tailLines

• tdbQuery

• textHistogram

• tickToDate

• toLower

• toUpper

• trfBig

• twoBitDup

• twoBitInfo

• twoBitMask

• twoBitToFa

• validateFiles

• validateManifest

• wigCorrelate

• wigEncode

• wigToBigWig

• wordLine

• xmlCat

• xmlToSql

Module

You can load the modules by:

module load biocontainers
module load kentutils

Example job

Warning

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 kentutils on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=kentutils
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers kentutils