RNASeqR
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

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RNASeqReadProcess: RNASeqReadProcess

RNASeqReadProcess: RNASeqReadProcess
In RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

Description Usage Arguments Value Author(s) Examples

View source: R/cmd_batch_rnaseq_raw_read_process.R

Description

Process raw reads for RNA-Seq workflow in R shell
This function do 5 things :

  1. 'Hisat2' : aligns raw reads to reference genome. If indices.optional in RNASeqRParam is FALSE, Hisat2 indices will be created.

  2. 'Rsamtools': converts '.sam' files to '.bam' files.

  3. 'Stringtie': assembles alignments into transcript.

  4. 'Gffcompare': examines how transcripts compare with the reference annotation.

  5. 'Stringtie': creates input files for ballgown, edgeR and DESeq2.

  6. raw reads count: create raw reads count for DESeq2 and edgeR

Before running this function, RNASeqEnvironmentSet_CMD() or RNASeqEnvironmentSet() must be executed successfully. If you want to process raw reads for the following RNA-Seq workflow in background, please see RNASeqReadProcess_CMD() function.

Usage

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RNASeqReadProcess(RNASeqRParam, which.trigger = "OUTSIDE",
  INSIDE.path.prefix = NA, SAMtools.or.Rsamtools = "Rsamtools",
  Hisat2.Index.run = TRUE, Hisat2.Index.num.parallel.threads = "1",
  Hisat2.Index.large.index = FALSE,
  Hisat2.Index.local.ftab.chars = "6",
  Hisat2.Index.local.off.rate = "3", Hisat2.Index.ftab.chars = "10",
  Hisat2.Index.off.rate = "4", Hisat2.Alignment.run = TRUE,
  Hisat2.Alignment.num.parallel.threads = "1",
  Hisat2.Alignment.skip = "0", Hisat2.Alignment.trim5 = "0",
  Hisat2.Alignment.trim3 = "0",
  Hisat2.Alignment.n.ceil.1.function.type = "L",
  Hisat2.Alignment.n.ceil.2.constant.term = "0",
  Hisat2.Alignment.n.ceil.3.coefficient = "0.15",
  Hisat2.Alignment.mp.MX = "6", Hisat2.Alignment.mp.MN = "2",
  Hisat2.Alignment.sp.MX = "2", Hisat2.Alignment.sp.MN = "1",
  Hisat2.Alignment.np = "1", Hisat2.Alignment.rdg.1 = "5",
  Hisat2.Alignment.rdg.2 = "3", Hisat2.Alignment.rfg.1 = "5",
  Hisat2.Alignment.rfg.2 = "3",
  Hisat2.Alignment.score.min.1.function.type = "L",
  Hisat2.Alignment.score.min.2.constant.term = "0",
  Hisat2.Alignment.score.min.3.coefficient = "-0.2",
  Hisat2.Alignment.pen.cansplice = "0",
  Hisat2.Alignment.penc.noncansplice = "12",
  Hisat2.Alignment.pen.canintronlen.1.function.type = "G",
  Hisat2.Alignment.pen.canintronlen.2.constant.term = "-8",
  Hisat2.Alignment.pen.canintronlen.3.coefficient = "1",
  Hisat2.Alignment.pen.noncanintronlen.1.function.type = "G",
  Hisat2.Alignment.pen.noncanintronlen.2.constant.term = "-8",
  Hisat2.Alignment.pen.noncanintronlen.3.coefficient = "1",
  Hisat2.Alignment.min.intronlen = "20",
  Hisat2.Alignment.max.intronlen = "500000",
  Hisat2.Alignment.rna.strandness = "None", Hisat2.Alignment.k = "5",
  Hisat2.Alignment.max.seeds = "5", Hisat2.Alignment.secondary = FALSE,
  Hisat2.Alignment.minins = "0", Hisat2.Alignment.maxins = "500",
  Hisat2.Alignment.seed = "0", STAR.Index.num.parallel.threads = "1",
  STAR.Index.sjdbOverhang.Read.length = "100",
  STAR.Index.genomeSAindexNbases = "14",
  STAR.Index.genomeChrBinNbits = "18",
  STAR.Index.genomeSAsparseD = "1", STAR.Alignment.run = FALSE,
  STAR.Alignment.num.parallel.threads = "1",
  STAR.Alignment.genomeLoad = "NoSharedMemory",
  STAR.Alignment.readMapNumber = "-1",
  STAR.Alignment.clip3pNbases = "0", STAR.Alignment.clip5pNbases = "0",
  STAR.Alignment.clip3pAdapterSeq = "-",
  STAR.Alignment.clip3pAdapterMMp = "0.1",
  STAR.Alignment.clip3pAfterAdapterNbases = "0",
  STAR.Alignment.limitGenomeGenerateRAM = "31000000000",
  STAR.Alignment.limitIObufferSize = "150000000",
  STAR.Alignment.limitOutSAMoneReadBytes = "100000",
  STAR.Alignment.limitOutSJoneRead = "1000",
  STAR.Alignment.limitOutSJcollapsed = "1000000",
  STAR.Alignment.limitBAMsortRAM = "0",
  STAR.Alignment.outReadsUnmapped = "None",
  STAR.Alignment.outQSconversionAdd = "0",
  STAR.Alignment.outSAMprimaryFlag = "OneBestScore",
  STAR.Alignment.outSAMmapqUnique = "255",
  STAR.Alignment.scoreGap = "0", STAR.Alignment.scoreGapNoncan = "-8",
  STAR.Alignment.scoreGapGCAG = "-4",
  STAR.Alignment.scoreGapATAC = "-8",
  STAR.Alignment.scoreGenomicLengthLog2scale = "-0.25",
  STAR.Alignment.scoreDelOpen = "-2",
  STAR.Alignment.scoreDelBase = "-2",
  STAR.Alignment.scoreInsOpen = "-2",
  STAR.Alignment.scoreInsBase = "-2",
  STAR.Alignment.scoreStitchSJshift = "1",
  STAR.Alignment.seedSearchStartLmax = "50",
  STAR.Alignment.seedSearchStartLmaxOverLread = "1.0",
  STAR.Alignment.seedSearchLmax = "0",
  STAR.Alignment.seedMultimapNmax = "10000",
  STAR.Alignment.seedPerReadNmax = "1000",
  STAR.Alignment.seedPerWindowNmax = "50",
  STAR.Alignment.seedNoneLociPerWindow = "10",
  STAR.Alignment.alignIntronMin = "21",
  STAR.Alignment.alignIntronMax = "0",
  STAR.Alignment.alignMatesGapMax = "0",
  STAR.Alignment.alignSJoverhangMin = "5",
  STAR.Alignment.alignSJDBoverhangMin = "3",
  STAR.Alignment.alignSplicedMateMapLmin = "0",
  STAR.Alignment.alignSplicedMateMapLminOverLmate = "0.66",
  STAR.Alignment.alignWindowsPerReadNmax = "10000",
  STAR.Alignment.alignTranscriptsPerWindowNmax = "100",
  STAR.Alignment.alignTranscriptsPerReadNmax = "10000",
  STAR.Alignment.alignEndsType = "Local",
  STAR.Alignment.winAnchorMultimapNmax = "50",
  STAR.Alignment.winBinNbits = "16",
  STAR.Alignment.winAnchorDistNbins = "9",
  STAR.Alignment.winFlankNbins = "4", Rsamtools.Bam.run = TRUE,
  Samtools.Bam.num.parallel.threads = "1", Rsamtools.nCores = "1",
  StringTie.Assemble.run = TRUE,
  Stringtie.Assembly.num.parallel.threads = "1",
  Stringtie.Assembly.f = "0.1", Stringtie.Assembly.m = "200",
  Stringtie.Assembly.c = "2.5", Stringtie.Assembly.g = "50",
  Stringtie.Assembly.M = "0.95", StringTie.Merge.Trans.run = TRUE,
  Stringtie.Merge.num.parallel.threads = "1",
  Gffcompare.Ref.Sample.run = TRUE, StringTie.Ballgown.run = TRUE,
  Stringtie.2.Ballgown.num.parallel.threads = "1",
  PreDECountTable.run = TRUE, check.s4.print = TRUE)

Arguments

RNASeqRParam

S4 object instance of experiment-related parameters

which.trigger

Default value is OUTSIDE. User should not change this value.

INSIDE.path.prefix

Default value is NA. User should not change this value.

SAMtools.or.Rsamtools

Default value is Rsamtools. User can set to SAMtools to use command-line-based 'samtools' instead.

Hisat2.Index.run

Whether to run 'HISAT2 index' step in this function step. Default value is TRUE. Set FALSE to skip 'HISAT2 index' step.

Hisat2.Index.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Hisat2 index step. The default is "1"

Hisat2.Index.large.index

Hisat2 index terminal '–large-index' option. Default value is FALSE

Hisat2.Index.local.ftab.chars

Hisat2 index terminal '-t/–ftabchars' option. Default value is "6"

Hisat2.Index.local.off.rate

Hisat2 index terminal '–localoffrate' option. Default value is "3"

Hisat2.Index.ftab.chars

Hisat2 index terminal '–localftabchars' option. Default value is "10"

Hisat2.Index.off.rate

Hisat2 index terminal '–offrate' option. Default value is "4"

Hisat2.Alignment.run

Whether to run 'HISAT2 alignment' step in this function step. Default value is TRUE. Set FALSE to skip 'HISAT2 alignment' step.

Hisat2.Alignment.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Hisat2 alignment step. The default is "1"

Hisat2.Alignment.skip

Hisat2 alignment terminal '-s/–skip' option. Default value is "0"

Hisat2.Alignment.trim5

Hisat2 alignment terminal '-5/–trim5' option. Default value is "0"

Hisat2.Alignment.trim3

Hisat2 alignment terminal '-3/–trim3' option. Default value is "0"

Hisat2.Alignment.n.ceil.1.function.type

Hisat2 alignment terminal '–n-ceil' option. Default value is "L"

Hisat2.Alignment.n.ceil.2.constant.term

Hisat2 alignment terminal '–n-ceil' option. Default value is "0"

Hisat2.Alignment.n.ceil.3.coefficient

Hisat2 alignment terminal '–n-ceil' option. Default value is "0.15"

Hisat2.Alignment.mp.MX

Hisat2 alignment terminal '–mp MX' option. Default value is "6"

Hisat2.Alignment.mp.MN

Hisat2 alignment terminal '–mp MN' option. Default value is "2"

Hisat2.Alignment.sp.MX

Hisat2 alignment terminal '–sp MX' option. Default value is "2"

Hisat2.Alignment.sp.MN

Hisat2 alignment terminal '–sp MN' option. Default value is "1"

Hisat2.Alignment.np

Hisat2 alignment terminal '–np' option. Default value is "1"

Hisat2.Alignment.rdg.1

Hisat2 alignment terminal '–rdg' first option. Default value is "5"

Hisat2.Alignment.rdg.2

Hisat2 alignment terminal '–rdg' first option. Default value is "3"

Hisat2.Alignment.rfg.1

Hisat2 alignment terminal '–rfg' first option. Default value is "5"

Hisat2.Alignment.rfg.2

Hisat2 alignment terminal '–rfg' first option. Default value is "3"

Hisat2.Alignment.score.min.1.function.type

Hisat2 alignment terminal '–rdg' first option. Default value is "L"

Hisat2.Alignment.score.min.2.constant.term

Hisat2 alignment terminal '–rdg' first option. Default value is "0"

Hisat2.Alignment.score.min.3.coefficient

Hisat2 alignment terminal '–rdg' first option. Default value is "-0.2"

Hisat2.Alignment.pen.cansplice

Hisat2 alignment terminal '–pen-cansplice' first option. Default value is "-0"

Hisat2.Alignment.penc.noncansplice

Hisat2 alignment terminal '–pen-noncansplice' option. Default value is "12"

Hisat2.Alignment.pen.canintronlen.1.function.type

Hisat2 alignment terminal '–pen-canintronlen' first option. Default value is "G"

Hisat2.Alignment.pen.canintronlen.2.constant.term

Hisat2 alignment terminal '–pen-canintronlen' second option. Default value is "-8"

Hisat2.Alignment.pen.canintronlen.3.coefficient

Hisat2 alignment terminal '–pen-canintronlen' third option. Default value is "1"

Hisat2.Alignment.pen.noncanintronlen.1.function.type

Hisat2 alignment terminal '–pen-noncanintronlen' first option. Default value is "G"

Hisat2.Alignment.pen.noncanintronlen.2.constant.term

Hisat2 alignment terminal '–pen-noncanintronlen' second option. Default value is "-8"

Hisat2.Alignment.pen.noncanintronlen.3.coefficient

Hisat2 alignment terminal '–pen-noncanintronlen' third option. Default value is "1"

Hisat2.Alignment.min.intronlen

Hisat2 alignment terminal '–min-intronlen' option. Default value is "20"

Hisat2.Alignment.max.intronlen

Hisat2 alignment terminal '–max-intronlen' option. Default value is "20"

Hisat2.Alignment.rna.strandness

Hisat2 alignment terminal '–rna-strandness' option. Default value is "None"

Hisat2.Alignment.k

Hisat2 alignment terminal '-k' option. Default value is "5"

Hisat2.Alignment.max.seeds

Hisat2 alignment terminal '–max-seeds' option. Default value is "5"

Hisat2.Alignment.secondary

Hisat2 alignment terminal '–secondary' option. Default value is "FALSE"

Hisat2.Alignment.minins

Hisat2 alignment terminal '-I/–minins' option. Default value is "0"

Hisat2.Alignment.maxins

Hisat2 alignment terminal '-X/–maxins' option. Default value is "500"

Hisat2.Alignment.seed

Hisat2 alignment terminal '-X/–maxins' option. Default value is "0"

STAR.Index.num.parallel.threads

Specify the number of processing threads (CPUs) to use for STAR index step. The default is "1"

STAR.Index.sjdbOverhang.Read.length

STAR index terminal '–sjdbOverhang' option. Default value is "100"

STAR.Index.genomeSAindexNbases

STAR index terminal '–genomeSAindexNbases' option. Default value is "14"

STAR.Index.genomeChrBinNbits

STAR index terminal '–genomeChrBinNbits' option. Default value is "18"

STAR.Index.genomeSAsparseD

STAR index terminal '–genomeSAsparseD' option. Default value is "1"

STAR.Alignment.run

Whether to run 'STAR index' step in this function step. Default value is FALSE. Set TRUE to run STAR alignment step. (need to set Hisat2.Index.run to FALSE)

STAR.Alignment.num.parallel.threads

Specify the number of processing threads (CPUs) to use for STAR alignment step. The default is "1"

STAR.Alignment.genomeLoad

STAR alignment terminal '–genomeLoad' option. Default value is "NoSharedMemory"

STAR.Alignment.readMapNumber

STAR alignment terminal '–readMapNumber' option. Default value is "-1"

STAR.Alignment.clip3pNbases

STAR alignment terminal '–clip3pNbases' option. Default value is "0"

STAR.Alignment.clip5pNbases

STAR alignment terminal '–clip5pNbases' option. Default value is "0"

STAR.Alignment.clip3pAdapterSeq

STAR alignment terminal '–clip3pAdapterSeq' option. Default value is "-"

STAR.Alignment.clip3pAdapterMMp

STAR alignment terminal '–clip3pAdapterMMp' option. Default value is "0.1"

STAR.Alignment.clip3pAfterAdapterNbases

STAR alignment terminal '–clip3pAfterAdapterNbases' option. Default value is "0"

STAR.Alignment.limitGenomeGenerateRAM

STAR alignment terminal '–limitGenomeGenerateRAM' option. Default value is "31000000000"

STAR.Alignment.limitIObufferSize

STAR alignment terminal '–limitIObufferSize' option. Default value is "150000000"

STAR.Alignment.limitOutSAMoneReadBytes

STAR alignment terminal '–limitOutSAMoneReadBytes' option. Default value is "100000"

STAR.Alignment.limitOutSJoneRead

STAR alignment terminal '–limitOutSJoneRead' option. Default value is "1000"

STAR.Alignment.limitOutSJcollapsed

STAR alignment terminal '–limitOutSJcollapsed' option. Default value is "1000000"

STAR.Alignment.limitBAMsortRAM

STAR alignment terminal '–limitBAMsortRAM' option. Default value is "0"

STAR.Alignment.outReadsUnmapped

STAR alignment terminal '–outReadsUnmapped' option. Default value is "None"

STAR.Alignment.outQSconversionAdd

STAR alignment terminal '–outQSconversionAdd' option. Default value is "0"

STAR.Alignment.outSAMprimaryFlag

STAR alignment terminal '–outSAMprimaryFlag' option. Default value is "OneBestScore"

STAR.Alignment.outSAMmapqUnique

STAR alignment terminal '–outSAMmapqUnique' option. Default value is "255"

STAR.Alignment.scoreGap

STAR alignment terminal '–scoreGap' option. Default value is "0"

STAR.Alignment.scoreGapNoncan

STAR alignment terminal '–scoreGapNoncan' option. Default value is "-8"

STAR.Alignment.scoreGapGCAG

STAR alignment terminal '–scoreGapGCAG' option. Default value is "-4"

STAR.Alignment.scoreGapATAC

STAR alignment terminal '–scoreGapATAC' option. Default value is "-8"

STAR.Alignment.scoreGenomicLengthLog2scale

STAR alignment terminal '–scoreGenomicLengthLog2scale' option. Default value is "-0.25"

STAR.Alignment.scoreDelOpen

STAR alignment terminal '–scoreDelOpen' option. Default value is "-2"

STAR.Alignment.scoreDelBase

STAR alignment terminal '–scoreDelBase' option. Default value is "-2"

STAR.Alignment.scoreInsOpen

STAR alignment terminal '–scoreInsOpen' option. Default value is "-2"

STAR.Alignment.scoreInsBase

STAR alignment terminal '–scoreInsBase' option. Default value is "-2"

STAR.Alignment.scoreStitchSJshift

STAR alignment terminal '–scoreStitchSJshift' option. Default value is "1"

STAR.Alignment.seedSearchStartLmax

STAR alignment terminal '–scoreStitchSJshift' option. Default value is "50"

STAR.Alignment.seedSearchStartLmaxOverLread

STAR alignment terminal '–seedSearchStartLmaxOverLread' option. Default value is "1.0"

STAR.Alignment.seedSearchLmax

STAR alignment terminal '–seedSearchLmax' option. Default value is "0"

STAR.Alignment.seedMultimapNmax

STAR alignment terminal '–seedMultimapNmax' option. Default value is "10000"

STAR.Alignment.seedPerReadNmax

STAR alignment terminal '–seedPerReadNmax' option. Default value is "1000"

STAR.Alignment.seedPerWindowNmax

STAR alignment terminal '–seedPerWindowNmax' option. Default value is "50"

STAR.Alignment.seedNoneLociPerWindow

STAR alignment terminal '–seedNoneLociPerWindow' option. Default value is "10"

STAR.Alignment.alignIntronMin

STAR alignment terminal '–alignIntronMin' option. Default value is "21"

STAR.Alignment.alignIntronMax

STAR alignment terminal '–alignIntronMax' option. Default value is "0"

STAR.Alignment.alignMatesGapMax

STAR alignment terminal '–alignMatesGapMax' option. Default value is "0"

STAR.Alignment.alignSJoverhangMin

STAR alignment terminal '–alignSJoverhangMin' option. Default value is "5"

STAR.Alignment.alignSJDBoverhangMin

STAR alignment terminal '–alignSJDBoverhangMin' option. Default value is "3"

STAR.Alignment.alignSplicedMateMapLmin

STAR alignment terminal '–alignSplicedMateMapLmin' option. Default value is "0"

STAR.Alignment.alignSplicedMateMapLminOverLmate

STAR alignment terminal '–alignSplicedMateMapLminOverLmate' option. Default value is "0.66"

STAR.Alignment.alignWindowsPerReadNmax

STAR alignment terminal '–alignWindowsPerReadNmax' option. Default value is "10000"

STAR.Alignment.alignTranscriptsPerWindowNmax

STAR alignment terminal '–alignTranscriptsPerWindowNmax' option. Default value is "100"

STAR.Alignment.alignTranscriptsPerReadNmax

STAR alignment terminal '–alignTranscriptsPerReadNmax' option. Default value is "10000"

STAR.Alignment.alignEndsType

STAR alignment terminal '–alignEndsType' option. Default value is "Local"

STAR.Alignment.winAnchorMultimapNmax

STAR alignment terminal '–winAnchorMultimapNmax' option. Default value is "50"

STAR.Alignment.winBinNbits

STAR alignment terminal '–winBinNbits' option. Default value is "16"

STAR.Alignment.winAnchorDistNbins

STAR alignment terminal '–winAnchorDistNbins' option. Default value is "9"

STAR.Alignment.winFlankNbins

STAR alignment terminal '–winFlankNbins' option. Default value is "4"

Rsamtools.Bam.run

Whether to run 'Rsamtools SAM to BAM' step in this function step. Default value is TRUE. Set FALSE to skip 'Rsamtools SAM to BAM' step.

Samtools.Bam.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Samtools sam to bam step. The default is "1"

Rsamtools.nCores

The number of cores to use when running 'Rsamtools' step. Default value is 1

StringTie.Assemble.run

Whether to run 'StringTie assembly' step in this function step. Default value is TRUE. Set FALSE to skip 'StringTie assembly' step.

Stringtie.Assembly.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Stringtie assembly. The default is "1"

Stringtie.Assembly.f

Stringtie assembly terminal '-f' option. Default value is "0.1"

Stringtie.Assembly.m

Stringtie assembly terminal '-m' option. Default value is "200"

Stringtie.Assembly.c

Stringtie assembly terminal '-c' option. Default value is "2.5"

Stringtie.Assembly.g

Stringtie assembly terminal '-g' option. Default value is "50"

Stringtie.Assembly.M

Stringtie assembly terminal '-M' option. Default value is "0.95"

StringTie.Merge.Trans.run

Whether to run 'StringTie GTF merging' step in this function step. Default value is TRUE. Set FALSE to skip 'StringTie GTF merging' step.

Stringtie.Merge.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Stringtie merge step. The default is "1"

Gffcompare.Ref.Sample.run

Whether to run 'Gffcompare comparison' step in this function step. Default value is TRUE. Set FALSE to skip 'Gffcompare comparison' step.

StringTie.Ballgown.run

Whether to run 'StringTie ballgown creation' step in this function step. Default value is TRUE. Set FALSE to skip 'StringTie ballgown creation' step.

Stringtie.2.Ballgown.num.parallel.threads

Specify the number of processing threads (CPUs) to use for Stringtie to ballgown step. The default is "1"

PreDECountTable.run

Whether to run 'gene raw reads count creation' step in this function step. Default value is TRUE. Set FALSE to skip 'gene raw reads count creation' step.

check.s4.print

Default TRUE. If TRUE, the result of checking RNASeqRParam will be reported in 'Rscript_out/Environment_Set.Rout'. If FALSE, the result of checking RNASeqRParam will not be in 'Rscript_out/Environment_Set.Rout'.

Value

None

Author(s)

Kuan-Hao Chao

Examples

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data(yeast)
## Not run: 
## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
##(or\code{RNASeqEnvironmentSet()}) is executed successfully.
RNASeqReadProcess(RNASeqRParam         = yeast,
                  num.parallel.threads = 10)
## End(Not run)

RNASeqR documentation built on Nov. 8, 2020, 7:49 p.m.

Related to RNASeqReadProcess in RNASeqR...

RNASeqR index
README.md RNASeqR : RNA-Seq analysis based on one independent variable

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