SEQprocess: SEQprocess

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

Run the NGS data processing pipeline

Usage

SEQprocess(fastq.dir = NULL, output.dir = file.path(getwd(), "result",
  "SEQprocess_result"), argList = list(program.name = "SEQprocess"),
  project.name = "SEQprocess", type = c("WGS", "WES", "BarSEQ", "RSEQ",
  "miRSEQ"), pipeline = c("none", "GDC", "GATK", "BarSEQ", "Tuxedo",
  "miRSEQ"), mc.cores = 1, run.cmd = TRUE, report.mode = FALSE,
  config.fn = system.file("data/config.R", package = "SEQprocess"),
  qc = TRUE, trim.method = c("trim.galore", "cutadapt", "none"),
  align.method = c("bwa", "bowtie2", "tophat2", "star", "none"),
  build.transcriptome.idx = FALSE, tophat.thread.number = 4,
  bwa.method = c("mem", "aln"), bwa.thread.number = 4,
  star.thread.number = 8, rm.dup = c("MarkDuplicates", "BARCODE", "none"),
  realign = TRUE, variant.call.method = c("none", "gatk", "varscan2",
  "mutect2", "muse", "somaticsniper"), gatk.thread.number = 4,
  annotation.method = c("annovar", "vep", "none"), ref = "hg38",
  rseq.abundance.method = c("none", "cufflinks", "htseq"),
  cufflinks.gtf = c("G", "g"), cufflinks.thread.number = 4,
  RNAtype = c("mRNA", "miRNA"), CNV = FALSE, make.eSet = FALSE,
  eset2SummarizedExperiment = FALSE, mut.cnt.cutoff = 8,
  qc.dir = file.path(output.dir, "00_qc"), trim.dir = file.path(output.dir,
  "01_trim"), align.dir = file.path(output.dir, "02_align"),
  rmdup.dir = file.path(output.dir, "03_rmdup"),
  realign.dir = file.path(output.dir, "04_realign"),
  vcf.dir = file.path(output.dir, "05_vcf"),
  annot.dir = file.path(output.dir, "06_annot"),
  RNAquant.dir = file.path(output.dir, "07_RNAquant"),
  cnv.dir = file.path(output.dir, "08_cnv"),
  Robject.dir = file.path(output.dir, "09_Robject"))

Arguments

fastq.dir	If the user starts the process with fastq files, set the directory for the fastq files.
output.dir	Output directory
argList	The argument list used by the user in the shell
project.name	User's project name
type	Sequence data type
pipeline	One of the six pipelines provided by SEQprocess
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.
run.cmd	Whether to execute the command line (default=TRUE)
report.mode	Whether the process is finished and report is generated
config.fn	Congifure file path
qc	Whether quality check
trim.method	Set trimming method
align.method	Set alignment method
build.transcriptome.idx	(tophat) A transcriptome index and the associated data files (the original GFF file) can be thus reused for multiple TopHat runs with this option, so these files are only created for the first run with a given set of transcripts. (default=FALSE)
tophat.thread.number	(tophat) A numeric value of the number of threads
bwa.method	(bwa) Set bwa method
bwa.thread.number	(bwa) A numeric value of the number of threads
star.thread.number	(STAR) A numeric value of the number of threads
rm.dup	Set the remove duplicates method
realign	Whether realignment
variant.call.method	Set variant call method
annotation.method	Set variant annotation method
ref	(annovar) Set annovar reference version
rseq.abundance.method	Set RNA quantification method
cufflinks.gtf	(cufflinks) If you set "-G", Output will not include novel genes and isoforms that are assembled.
cufflinks.thread.number	(cufflinks) A numeric value of the number of threads
RNAtype	(htseq) Choose mRNA or miRNA.
CNV	Whether estimate copy number variation
make.eSet	Make ExpressionSet R data(RNA expression, Copy number variation, Mutation)
eset2SE	Convert ExpressionSet R data to SummarizedExperiment R data

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.