PoolQCbyRead: Evaluate QC by read

In aliafdz/QApckg: Quality assessment for Miseq data derived from viral sequencing

Evaluate QC by read

Description

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 FiltbyQ30 function.

Usage

PoolQCbyRead(flashfiles, samples, primers, ncores = 1)

Arguments

flashfiles	Vector including the paths of FLASH processed files, with fastq extension.
samples	Data frame with relevant information to identify the samples of the sequencing experiment, including Patient.ID, MID, Primer.ID, Region, RefSeq.ID, and Pool.Nm columns.
primers	Data frame with information about the primers used in the experiment, including Ampl.Nm, Region, Primer.FW, Primer.RV, FW.pos, RV.pos, FW.tpos, RV.tpos, Aa.ipos, and Aa.lpos columns.
ncores	Number of cores to use for parallelization with mclapply.hack.

Value

After execution a message will appear in console, indicating that the following report files have been generated (and saved in a reports folder):

1. 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.

2. PoolReadLengths.pdf: Includes one plot for each pool representing the read length distribution.

Author(s)

Alicia Aranda

See Also

R1R2toFLASH, QCscores

Examples

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)

aliafdz/QApckg documentation built on June 2, 2022, 10:29 a.m.