RNASeqReadProcess_CMD: RNASeqReadProcess_CMD
In HowardChao/RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
View source: R/cmd_batch_rnaseq_raw_read_process.R
RNASeqReadProcess_CMD R Documentation
RNASeqReadProcess_CMD
Description
Process raw reads for RNA-Seq workflow in background.
This function do 5 things :
'Hisat2' : aligns raw reads to reference genome.
If indices.optional in RNASeqRParam is
FALSE, Hisat2 indices will be created.
'Rsamtools': converts '.sam' files to '.bam' files.
'Stringtie': assembles alignments into transcript.
'Gffcompare': examines how transcripts compare with the
reference annotation.
'Stringtie': creates input files for ballgown, edgeR and DESeq2.
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 R shell, please see RNASeqReadProcess() function.
Usage
RNASeqReadProcess_CMD(RNASeqRParam, 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, run = TRUE, check.s4.print = TRUE)
Arguments
RNASeqRParam
S4 object instance of experiment-related
parameters
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.
run
Default value is TRUE. If TRUE,
'Rscript/Environment_Set.R' will be created and executed.
The output log will be stored in 'Rscript_out/Environment_Set.Rout'.
If False, 'Rscript/Environment_Set.R' will be
created without executed.
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
data(yeast)
## Not run:
## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
## (or\code{RNASeqEnvironmentSet()}) is executed successfully.
RNASeqReadProcess_CMD(RNASeqRParam = yeast,
num.parallel.threads = 10)
## End(Not run)
HowardChao/RNASeqR documentation built on May 5, 2022, 8:32 p.m.
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View source: R/cmd_batch_rnaseq_raw_read_process.R
| RNASeqReadProcess_CMD | R Documentation |
RNASeqReadProcess_CMD
Description
Process raw reads for RNA-Seq workflow in background.
This function do 5 things :
'Hisat2' : aligns raw reads to reference genome. If
indices.optionalinRNASeqRParamisFALSE, Hisat2 indices will be created.
'Rsamtools': converts '.sam' files to '.bam' files.
'Stringtie': assembles alignments into transcript.
'Gffcompare': examines how transcripts compare with the reference annotation.
'Stringtie': creates input files for ballgown, edgeR and DESeq2.
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 R shell, please see RNASeqReadProcess() function.
Usage
RNASeqReadProcess_CMD(RNASeqRParam, 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, run = TRUE, check.s4.print = TRUE)
Arguments
RNASeqRParam |
S4 object instance of experiment-related parameters |
SAMtools.or.Rsamtools |
Default value is |
Hisat2.Index.run |
Whether to run 'HISAT2 index' step in this function
step. Default value is |
Hisat2.Index.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Hisat2 index step. The default is |
Hisat2.Index.large.index |
Hisat2 index terminal '–large-index' option.
Default value is |
Hisat2.Index.local.ftab.chars |
Hisat2 index terminal '-t/–ftabchars'
option. Default value is |
Hisat2.Index.local.off.rate |
Hisat2 index terminal '–localoffrate'
option. Default value is |
Hisat2.Index.ftab.chars |
Hisat2 index terminal '–localftabchars'
option. Default value is |
Hisat2.Index.off.rate |
Hisat2 index terminal '–offrate' option.
Default value is |
Hisat2.Alignment.run |
Whether to run 'HISAT2 alignment' step in this
function step. Default value is |
Hisat2.Alignment.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Hisat2 alignment step. The default is |
Hisat2.Alignment.skip |
Hisat2 alignment terminal '-s/–skip' option.
Default value is |
Hisat2.Alignment.trim5 |
Hisat2 alignment terminal '-5/–trim5' option.
Default value is |
Hisat2.Alignment.trim3 |
Hisat2 alignment terminal '-3/–trim3' option.
Default value is |
Hisat2.Alignment.n.ceil.1.function.type |
Hisat2 alignment terminal
'–n-ceil' option. Default value is |
Hisat2.Alignment.n.ceil.2.constant.term |
Hisat2 alignment terminal
'–n-ceil' option. Default value is |
Hisat2.Alignment.n.ceil.3.coefficient |
Hisat2 alignment terminal
'–n-ceil' option. Default value is |
Hisat2.Alignment.mp.MX |
Hisat2 alignment terminal '–mp MX' option.
Default value is |
Hisat2.Alignment.mp.MN |
Hisat2 alignment terminal '–mp MN' option.
Default value is |
Hisat2.Alignment.sp.MX |
Hisat2 alignment terminal '–sp MX' option.
Default value is |
Hisat2.Alignment.sp.MN |
Hisat2 alignment terminal '–sp MN' option.
Default value is |
Hisat2.Alignment.np |
Hisat2 alignment terminal '–np' option.
Default value is |
Hisat2.Alignment.rdg.1 |
Hisat2 alignment terminal '–rdg' first option.
Default value is |
Hisat2.Alignment.rdg.2 |
Hisat2 alignment terminal '–rdg' first option.
Default value is |
Hisat2.Alignment.rfg.1 |
Hisat2 alignment terminal '–rfg' first option.
Default value is |
Hisat2.Alignment.rfg.2 |
Hisat2 alignment terminal '–rfg' first option.
Default value is |
Hisat2.Alignment.score.min.1.function.type |
Hisat2 alignment terminal
'–rdg' first option. Default value is |
Hisat2.Alignment.score.min.2.constant.term |
Hisat2 alignment terminal
'–rdg' first option. Default value is |
Hisat2.Alignment.score.min.3.coefficient |
Hisat2 alignment terminal
'–rdg' first option. Default value is |
Hisat2.Alignment.pen.cansplice |
Hisat2 alignment terminal
'–pen-cansplice' first option. Default value is |
Hisat2.Alignment.penc.noncansplice |
Hisat2 alignment terminal
'–pen-noncansplice' option. Default value is |
Hisat2.Alignment.pen.canintronlen.1.function.type |
Hisat2 alignment
terminal '–pen-canintronlen' first option. Default value is |
Hisat2.Alignment.pen.canintronlen.2.constant.term |
Hisat2 alignment
terminal '–pen-canintronlen' second option. Default value is |
Hisat2.Alignment.pen.canintronlen.3.coefficient |
Hisat2 alignment
terminal '–pen-canintronlen' third option. Default value is |
Hisat2.Alignment.pen.noncanintronlen.1.function.type |
Hisat2 alignment
terminal '–pen-noncanintronlen' first option. Default value is |
Hisat2.Alignment.pen.noncanintronlen.2.constant.term |
Hisat2 alignment
terminal '–pen-noncanintronlen' second option. Default value is |
Hisat2.Alignment.pen.noncanintronlen.3.coefficient |
Hisat2 alignment
terminal '–pen-noncanintronlen' third option. Default value is |
Hisat2.Alignment.min.intronlen |
Hisat2 alignment terminal
'–min-intronlen' option. Default value is |
Hisat2.Alignment.max.intronlen |
Hisat2 alignment terminal '–max-intronlen'
option. Default value is |
Hisat2.Alignment.rna.strandness |
Hisat2 alignment terminal '–rna-strandness'
option. Default value is |
Hisat2.Alignment.k |
Hisat2 alignment terminal '-k' option.
Default value is |
Hisat2.Alignment.max.seeds |
Hisat2 alignment terminal '–max-seeds' option.
Default value is |
Hisat2.Alignment.secondary |
Hisat2 alignment terminal '–secondary' option.
Default value is |
Hisat2.Alignment.minins |
Hisat2 alignment terminal '-I/–minins' option.
Default value is |
Hisat2.Alignment.maxins |
Hisat2 alignment terminal '-X/–maxins' option.
Default value is |
Hisat2.Alignment.seed |
Hisat2 alignment terminal '-X/–maxins' option.
Default value is |
STAR.Index.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for STAR index step. The default is |
STAR.Index.sjdbOverhang.Read.length |
STAR index terminal
'–sjdbOverhang' option. Default value is |
STAR.Index.genomeSAindexNbases |
STAR index terminal
'–genomeSAindexNbases' option. Default value is |
STAR.Index.genomeChrBinNbits |
STAR index terminal
'–genomeChrBinNbits' option. Default value is |
STAR.Index.genomeSAsparseD |
STAR index terminal
'–genomeSAsparseD' option. Default value is |
STAR.Alignment.run |
Whether to run 'STAR index' step in this function
step. Default value is |
STAR.Alignment.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for STAR alignment step. The default is |
STAR.Alignment.genomeLoad |
STAR alignment terminal '–genomeLoad'
option. Default value is |
STAR.Alignment.readMapNumber |
STAR alignment terminal '–readMapNumber'
option. Default value is |
STAR.Alignment.clip3pNbases |
STAR alignment terminal '–clip3pNbases'
option. Default value is |
STAR.Alignment.clip5pNbases |
STAR alignment terminal '–clip5pNbases'
option. Default value is |
STAR.Alignment.clip3pAdapterSeq |
STAR alignment terminal '–clip3pAdapterSeq'
option. Default value is |
STAR.Alignment.clip3pAdapterMMp |
STAR alignment terminal '–clip3pAdapterMMp'
option. Default value is |
STAR.Alignment.clip3pAfterAdapterNbases |
STAR alignment terminal
'–clip3pAfterAdapterNbases' option. Default value is |
STAR.Alignment.limitGenomeGenerateRAM |
STAR alignment terminal
'–limitGenomeGenerateRAM' option. Default value is |
STAR.Alignment.limitIObufferSize |
STAR alignment terminal
'–limitIObufferSize' option. Default value is |
STAR.Alignment.limitOutSAMoneReadBytes |
STAR alignment terminal
'–limitOutSAMoneReadBytes' option. Default value is |
STAR.Alignment.limitOutSJoneRead |
STAR alignment terminal
'–limitOutSJoneRead' option. Default value is |
STAR.Alignment.limitOutSJcollapsed |
STAR alignment terminal
'–limitOutSJcollapsed' option. Default value is |
STAR.Alignment.limitBAMsortRAM |
STAR alignment terminal
'–limitBAMsortRAM' option. Default value is |
STAR.Alignment.outReadsUnmapped |
STAR alignment terminal
'–outReadsUnmapped' option. Default value is |
STAR.Alignment.outQSconversionAdd |
STAR alignment terminal
'–outQSconversionAdd' option. Default value is |
STAR.Alignment.outSAMprimaryFlag |
STAR alignment terminal
'–outSAMprimaryFlag' option. Default value is |
STAR.Alignment.outSAMmapqUnique |
STAR alignment terminal
'–outSAMmapqUnique' option. Default value is |
STAR.Alignment.scoreGap |
STAR alignment terminal
'–scoreGap' option. Default value is |
STAR.Alignment.scoreGapNoncan |
STAR alignment terminal
'–scoreGapNoncan' option. Default value is |
STAR.Alignment.scoreGapGCAG |
STAR alignment terminal
'–scoreGapGCAG' option. Default value is |
STAR.Alignment.scoreGapATAC |
STAR alignment terminal
'–scoreGapATAC' option. Default value is |
STAR.Alignment.scoreGenomicLengthLog2scale |
STAR alignment terminal
'–scoreGenomicLengthLog2scale' option. Default value is |
STAR.Alignment.scoreDelOpen |
STAR alignment terminal
'–scoreDelOpen' option. Default value is |
STAR.Alignment.scoreDelBase |
STAR alignment terminal
'–scoreDelBase' option. Default value is |
STAR.Alignment.scoreInsOpen |
STAR alignment terminal
'–scoreInsOpen' option. Default value is |
STAR.Alignment.scoreInsBase |
STAR alignment terminal
'–scoreInsBase' option. Default value is |
STAR.Alignment.scoreStitchSJshift |
STAR alignment terminal
'–scoreStitchSJshift' option. Default value is |
STAR.Alignment.seedSearchStartLmax |
STAR alignment terminal
'–scoreStitchSJshift' option. Default value is |
STAR.Alignment.seedSearchStartLmaxOverLread |
STAR alignment terminal
'–seedSearchStartLmaxOverLread' option. Default value is |
STAR.Alignment.seedSearchLmax |
STAR alignment terminal
'–seedSearchLmax' option. Default value is |
STAR.Alignment.seedMultimapNmax |
STAR alignment terminal
'–seedMultimapNmax' option. Default value is |
STAR.Alignment.seedPerReadNmax |
STAR alignment terminal
'–seedPerReadNmax' option. Default value is |
STAR.Alignment.seedPerWindowNmax |
STAR alignment terminal
'–seedPerWindowNmax' option. Default value is |
STAR.Alignment.seedNoneLociPerWindow |
STAR alignment terminal
'–seedNoneLociPerWindow' option. Default value is |
STAR.Alignment.alignIntronMin |
STAR alignment terminal
'–alignIntronMin' option. Default value is |
STAR.Alignment.alignIntronMax |
STAR alignment terminal
'–alignIntronMax' option. Default value is |
STAR.Alignment.alignMatesGapMax |
STAR alignment terminal
'–alignMatesGapMax' option. Default value is |
STAR.Alignment.alignSJoverhangMin |
STAR alignment terminal
'–alignSJoverhangMin' option. Default value is |
STAR.Alignment.alignSJDBoverhangMin |
STAR alignment terminal
'–alignSJDBoverhangMin' option. Default value is |
STAR.Alignment.alignSplicedMateMapLmin |
STAR alignment terminal
'–alignSplicedMateMapLmin' option. Default value is |
STAR.Alignment.alignSplicedMateMapLminOverLmate |
STAR alignment terminal
'–alignSplicedMateMapLminOverLmate' option. Default value is |
STAR.Alignment.alignWindowsPerReadNmax |
STAR alignment terminal
'–alignWindowsPerReadNmax' option. Default value is |
STAR.Alignment.alignTranscriptsPerWindowNmax |
STAR alignment terminal
'–alignTranscriptsPerWindowNmax' option. Default value is |
STAR.Alignment.alignTranscriptsPerReadNmax |
STAR alignment terminal
'–alignTranscriptsPerReadNmax' option. Default value is |
STAR.Alignment.alignEndsType |
STAR alignment terminal
'–alignEndsType' option. Default value is |
STAR.Alignment.winAnchorMultimapNmax |
STAR alignment terminal
'–winAnchorMultimapNmax' option. Default value is |
STAR.Alignment.winBinNbits |
STAR alignment terminal
'–winBinNbits' option. Default value is |
STAR.Alignment.winAnchorDistNbins |
STAR alignment terminal
'–winAnchorDistNbins' option. Default value is |
STAR.Alignment.winFlankNbins |
STAR alignment terminal
'–winFlankNbins' option. Default value is |
Rsamtools.Bam.run |
Whether to run 'Rsamtools SAM to BAM' step in this
function step. Default value is |
Samtools.Bam.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Samtools sam to bam step. The default is |
Rsamtools.nCores |
The number of cores to use when running
'Rsamtools' step. Default value is |
StringTie.Assemble.run |
Whether to run 'StringTie assembly' step in
this function step. Default value is |
Stringtie.Assembly.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Stringtie assembly. The default is |
Stringtie.Assembly.f |
Stringtie assembly terminal
'-f' option. Default value is |
Stringtie.Assembly.m |
Stringtie assembly terminal
'-m' option. Default value is |
Stringtie.Assembly.c |
Stringtie assembly terminal
'-c' option. Default value is |
Stringtie.Assembly.g |
Stringtie assembly terminal
'-g' option. Default value is |
Stringtie.Assembly.M |
Stringtie assembly terminal
'-M' option. Default value is |
StringTie.Merge.Trans.run |
Whether to run 'StringTie GTF merging' step
in this function step. Default value is |
Stringtie.Merge.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Stringtie merge step. The default is |
Gffcompare.Ref.Sample.run |
Whether to run 'Gffcompare comparison' step
in this function step. Default value is |
StringTie.Ballgown.run |
Whether to run 'StringTie ballgown creation'
step in this function step. Default value is |
Stringtie.2.Ballgown.num.parallel.threads |
Specify the number of processing
threads (CPUs) to use for Stringtie to ballgown step. The default is |
PreDECountTable.run |
Whether to run 'gene raw reads count creation'
step in this function step. Default value is |
run |
Default value is |
check.s4.print |
Default |
Value
None
Author(s)
Kuan-Hao Chao
Examples
data(yeast)
## Not run:
## Before run this function, make sure \code{RNASeqEnvironmentSet_CMD()}
## (or\code{RNASeqEnvironmentSet()}) is executed successfully.
RNASeqReadProcess_CMD(RNASeqRParam = yeast,
num.parallel.threads = 10)
## End(Not run)
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