Quality control workflow

Table of Contents Resources Quality control workflow Quality control workflow Setup

Resources

• Workshop code
• An Introduction to ShortRead (Quality control page 8)

Quality control workflow

The ShortRead package contains a function called qa() which creates a quality report from several input formats, (usually a Fastq file).

 type=c("SolexaExport", "SolexaRealign", "Bowtie", "MAQMap", "MAQMapShort", "fastq", "BAM")

This function produces similar outputs to FastqQC but executes slightly faster. Functionality has been written to perform quality control either;

1. on a ShortReadQ structure of NGS reads loading into R using readFastq()
2. Specify the directory to run qa() directly from the NGS files.

Quality control workflow

Setup

The first command clears out any existing R objects from your current workspace

 # Clear working directory objects
 rm(list=ls())

Any contributed libraries need to be installed once, but loaded each time they are used with either require(), or library();

require(ShortRead)

Loading help documentation vignette;

 # Getting vignette help
 if(interactive()) vignette("Overview") ## Quality assessment, page 8 

The next commands source some global variables in the file ~/VISG-course-2012/supplementary_QC/globals.R

# Globals
cat("[ Code to source() ]\n")
cat(readLines("globals.R"), sep="\n")

# source globals code
source("globals.R")

cat("[ Directory and Fastq filenames ]\n")
print(indir)
print(fileNames)