This function evaluates fastq files after the execution of the FLASH program to extend
paired-end reads, and returns QC by read plots in pdf format. The results of this function are
important for defining the maximum fraction of bases below Q30 allowed in reads, which will
be used in
PoolQCbyRead(flashfiles, samples, primers, ncores = 1)
Vector including the paths of FLASH processed files, with fastq extension.
Data frame with relevant information to identify the samples of the sequencing experiment, including
Data frame with information about the primers used in the experiment, including
Number of cores to use for parallelization with
After execution a message will appear in console, indicating that the following report files have been generated (and saved in a reports folder):
PoolQCbyRead_PoolName.pdf: This file is generated for each pool used in the
experiment, after extracting its name from
samples data frame. The pdf includes
includes a representation of bases below Q30 (in nº of reads and percentage) by read.
PoolReadLengths.pdf: Includes one plot for each pool representing the read length distribution.
flashDir <- "./flash" repDir <- "./reports" # Save the file names with complete path flashfiles <- list.files(flashDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) # Get data samples <- read.table("./data/samples.csv", sep="\t", header=T, colClasses="character",stringsAsFactors=F) primers <- read.table("./data/primers.csv", sep="\t", header=T, stringsAsFactors=F) PoolQCbyRead(flashfiles,samples,primers)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.