runFC: Run featureCounts on a set of bam files

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

Description

Run featureCounts on a set of bam files

Usage

runFC(projName, bamDir, fileList, outFile, ncores = 16,
  subreadMod = "apps/subread/1.5.0-p3/gcc-4.4.7",
  refDir = "/scratch/pschofield/ref/star/GRCh37_pa",
  annoFile = file.path(refDir, "Homo_sapiens.GRCh37.85.gtf"),
  genomeFile = file.path(refDir,
  "Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa"),
  switches = " -M -O -C -P -p -t exon -g transcript_id -f -d 50")

Arguments

projName	project name
bamDir	location of bamfiles (actually directory where counting takes place)
fileList	list of files if not full paths will have to be in bamDir but can be fully qualified paths
outFile	name of output file
ncores	number of cores to use
annoFile	the gtf annotation file to count against must of course match the alignment reference
switches	extra switches for featureCounts for example paired end or exon counting

PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.