runJAFFA: run JAFFA fusion gene detection

In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

Description

run JAFFA fusion gene detection

Usage

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 May 6, 2019, 6:45 p.m.