alignSubread: Simple subread aligner

Description Usage Arguments

View source: R/alignSubread.R

Description

This is a simpler subread aligner that runs of single fastq files rather than individual lane fastqs from the HiSeq. There maybe QC advantages of aligning the individual fastqc but sometimes it is just simpler to merge before the event.

Usage

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alignSubread(fileName, projName, runId,
  outRoot = file.path("/scratch/pschofield/Projects", projName),
  outName = "Data/alignments/subread", noSub = F, scpIt = T,
  subreadMod = "apps/subread/1.5.0-p3/gcc-4.4.7",
  samtoolsMod = "apps/samtools/1.2/gcc/4.4.7", mem = "32Gb",
  stranded = "fr", nmap = "2", itype = 1, refGenome = NULL,
  ncores = 16, fqExt = ".fastq", pe = T)

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.