Package: rlpipes
RLPipesRLPipesis an upstream workflow for R-loop-mapping data.The primary outputs of the pipeline are:Coverage (.bw) tracksPeaks (.broadpeak) filesAlignment (.bam) filesRLSeqreport (.html and .rda) filesFollowing RLPipes, theRLSeqR
package can be used for more fine-grained downstream analysis.InstallThe preferred installation method ismambaorconda(slower):mambacreate-nrlpipes-cbioconda-cconda-forgerlpipes
condaactivaterlpipesUsingpipRLPipes can also be installed withpip. However, system dependencies will
still need to be installed. To accomplish this, do the following:gitclonehttps://github.com/Bishop-Laboratory/RLPipes.gitcdRLPipes/
condainstall-cconda-forgemamba-y
mambaenvcreate-frlpipes.yml--force
condaactivaterlpipes
python-mpipinstall-e.Basic UsageTo run RLPipes, you will need asamples.csvfile that describes your samples.
Here is an example file provided for testing purposes:experimentcontrolSRX113814SRX1025890SRX1025893SRX1025899The basic usage of RSeq follows a three-step process:build,check, andrun.BuildRLPipes buildgenerates aconfig.jsonfile that controls the underlyingsnakemakeworkflow.RLPipesbuild-mDRIPrlpipes_out/tests/test_data/samples.csvOutput:Success!RSeqhasbeeninitializedatthespecifieddirectory:rlpipes_out/

Run'RLPipes check rlpipes_out/'toverifytheconfiguration.CheckVerifies that the run will succeed and generates a plot of the workflow jobs.RLPipescheckrlpipes_out/Output:Success!TheDAGhasbeengeneratedsuccessfully.Youcanviewithere:rlpipes_out/dag.png

Run'RLPipes run rlpipes_out/'toexecutetheworkflow.RunExecutes the workflow rules.RLPipesrunrlpipes_out/If multiple cores are available, they can be specified using the--threads/-toption.RLPipesrun-t30rlpipes_out/Usage ReferenceTop-level usage:Usage:RLPipes[OPTIONS]COMMAND[ARGS]...RSeq:AnR-loopmappingpipelinewithbuilt-inQC.

Options:--versionShowtheversionandexit.--helpShowthismessageandexit.

Commands:buildConfigureanRSeqworkflow.checkValidateanRSeqworkflow.runExecuteanRSeqworkflow.BuildUsage:RLPipesbuild[OPTIONS]RUN_DIRSAMPLESConfigureanRLPipesworkflow.RUN_DIR:DirectoryforRLPipesExecution.Willbecreatedifitdoesnotexist.SAMPLES:ACSVfilewithatleastonecolumn"experiment"thatprovidesthepathtoeitherlocalfastqfiles,bamfiles,orpublicsampleaccessions(SRXorGSM).Inputcontrolsshouldbeinthe"control"column.Ifprovidingpaired-endfastqfiles,enter:"exp_1.fastq~exp_2.fastq".Columnsmayalsoinclude"genome"and"mode"columns.Thesewilloverridethe-g,-m,and-noptions."genome"(-g/--genome)isnotrequiredifprovidingpublicdataaccessions.Example#1: "RLPipes build -m DRIP outdir/ samples.csv"samples.csv:experimentSRX113812SRX113813Example#2: "RLPipes build outdir/ samples.csv"samples.csv:experiment,control,genome,modeqDRIP_siGL3_1.fq~qDRIP_siGL3_2.fq,,hg38,qDRIPDRIPc_3T3.fq,Input_3T3.fq,mm10,DRIPc



Options:-m,--modeTEXTThetypeofsequencing(e.g.,"DRIP").Theavailableoptionsarecurrently:DRIP,DRIPc,qDRIP,sDRIP,ssDRIP,R-ChIP,RR-ChIP,RDIP,S1-DRIP,DRIVE,RNH-CnR,andMapR-g,--genomeTEXTUCSCgenomeforsamples(e.g.,'hg38').Notrequiredifprovidingpublicdataaccessions.-n,--nameTEXTSamplenamesforuseinoutputreport.Bydefault,inferredfrominputs.--helpShowthismessageandexit.CheckUsage:RLPipescheck[OPTIONS]RUN_DIRValidateanRLPipesworkflow.RUN_DIR:Directoryconfiguredwith`RLPipesbuild`andreadyforcheckingandexecution.

Options:-s,--smargsTEXTDictofargumentspassedtothesnakemakepythonAPI.Default:"{'use_conda': True}".ReadthesnakemakeAPIreferenceforthefulllistofoptions.-t,--threadsINTEGERNumberofthreadstouse.Default:1--bwamem2AlignwithBWA-MEM2insteadofBWA.BWAMEM2Needs>70GBRAMavaialbletobuildindex,butshows>3xspeedincrease.Default:False.--macs2Callpeaksusingmacs2insteadofmacs2-G,--groupbyTEXTColumn(s)whichidentifybiologically-meaningfulgrouping(s)ofsamples(i.e.,conditions).Canbeanycolumnnamefromthe`samples`CSVfile.Ifusingpublicdataaccessions,itmayalsoinclude"study".NOTE:If--groupbyissetandthereR-loop-mappingandexpressionsampleswithingroups,expression-matchedanalysiswillberun.Thiscanbedisabledwiththe--noexpflag.Example#1: "RSeqCLI build outdir/ samples.csv--groupcolstissue"samples.csv:experiment, mode, tissueGSM1720615, DRIP, NT2GSM1720616, DRIP, NT2GSM1720619, DRIP, K562Example #2: "RSeqCLIbuildoutdir/samples.csv--groupbytissue"samples.csv:experiment, mode, tissueGSM1720615, DRIP, NT2GSM1720616, DRIP, NT2GSM1720613, DRIPc, NT2GSM1720614, DRIPc, NT2GSM1720622, RNA-seq, NT2GSM1720623, RNA-seq, NT2--noexp                If set, no expression-matched analysis will beperformed.--noreport             If set, RLSeq reports will not be generated.--debug                Run pipeline on subsampled number of reads (fortesting).--tsv                  Obtain config from config.tsv file instead ofconfig.json.--noaws                If set, prefetch from SRA tools will be used todownload any public SRA data instead of AWS S3.--help                 Show this message and exit.RunUsage:RLPipesrun[OPTIONS]RUN_DIRExecuteanRLPipesworkflow.RUN_DIR:Directoryconfiguredwith`RLPipesbuild`andreadyforcheckingandexecution.

Options:-s,--smargsTEXTDictofargumentspassedtothesnakemakepythonAPI.Default:"{'use_conda': True}".ReadthesnakemakeAPIreferenceforthefulllistofoptions.-t,--threadsINTEGERNumberofthreadstouse.Default:1--bwamem2AlignwithBWA-MEM2insteadofBWA.BWAMEM2Needs>70GBRAMavaialbletobuildindex,butshows>3xspeedincrease.Default:False.--macs2Callpeaksusingmacs2insteadofmacs2-G,--groupbyTEXTColumn(s)whichidentifybiologically-meaningfulgrouping(s)ofsamples(i.e.,conditions).Canbeanycolumnnamefromthe`samples`CSVfile.Ifusingpublicdataaccessions,itmayalsoinclude"study".NOTE:If--groupbyissetandthereR-loop-mappingandexpressionsampleswithingroups,expression-matchedanalysiswillberun.Thiscanbedisabledwiththe--noexpflag.Example#1: "RSeqCLI build outdir/ samples.csv--groupcolstissue"samples.csv:experiment, mode, tissueGSM1720615, DRIP, NT2GSM1720616, DRIP, NT2GSM1720619, DRIP, K562Example #2: "RSeqCLIbuildoutdir/samples.csv--groupbytissue"samples.csv:experiment, mode, tissueGSM1720615, DRIP, NT2GSM1720616, DRIP, NT2GSM1720613, DRIPc, NT2GSM1720614, DRIPc, NT2GSM1720622, RNA-seq, NT2GSM1720623, RNA-seq, NT2--noexp                If set, no expression-matched analysis will beperformed.--noreport             If set, RLSeq reports will not be generated.--debug                Run pipeline on subsampled number of reads (fortesting).--tsv                  Obtain config from config.tsv file instead ofconfig.json.--help                 Show this message and exit.