runJAFFA: run JAFFA fusion gene detection

Description Usage Arguments

View source: R/runJAFFA.R

Description

run JAFFA fusion gene detection

Usage

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runJAFFA(sampleId, dataDir, filePattern, projName, outDir,
  refGenome = "hg19", refAnno = "genCode19", readLayout = "single",
  javaMod = "compilers/java/1.8.0_40/noarch",
  velvetMod = "apps/velvet/1.2.10/gcc-4.4.7",
  oasesMod = "apps/oases/0.2.08/gcc-4.4.7",
  blatMod = "apps/blat/35/gcc-4.4.7",
  samtoolsMod = "apps/samtools/0.1.19/gcc-4.4.7",
  bowtie2Mod = "apps/bowtie2/2.2.1/gcc/4.4.7",
  rMod = "apps/R/3.3.0/gcc-4.8.5",
  jaffaPath = "/scratch/pschofield/Projects/Sandbox/JAFFA-version-1.08",
  ncores = 2, mem = "32Gb", noSub = F)

Arguments

sampleId

id for naming the job script

dataDir

location of the fastq files

filePattern

file pattern to include all the relevant fastq files

projName

name of the project

outDir

full path to file output


PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.