runStarAlign: Submit a list of files associated with a project for bwa...

Description Usage Arguments

View source: R/runStarAlign.R

Description

Submit a list of files associated with a project for bwa alignment and deduping

Usage

1
2
3
4
5
6
runStarAlign(projName, sampleID, fileTable, runName,
  outRoot = file.path("/scratch/pschofield/Projects", projName),
  outName = "Data/alignment/star", noSub = F, scpIt = T,
  starMod = "apps/star/2.5.1b/gcc-5.1.0",
  samtoolsMod = "apps/samtools/0.1.19/gcc/4.4.7", refSequence = NULL,
  refGenome = NULL, ncores = 16, fqExt = ".fq", pe = T, jm = F)

Arguments

projName

project name

outRoot

output root directory

fileList

list of fastq file


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