Read quality filtering and trimming
The following removes reads with low quality base calls (here Phred scores below 20) from all FASTQ files.
args <- systemArgs(sysma="param/trimPE.param", mytargets="targetsPE.txt")[1:4] # Note: subsetting!
filterFct <- function(fq, cutoff=20, Nexceptions=0) {
qcount <- rowSums(as(quality(fq), "matrix") <= cutoff)
fq[qcount <= Nexceptions] # Retains reads where Phred scores are >= cutoff with N exceptions
}
preprocessReads(args=args, Fct="filterFct(fq, cutoff=20, Nexceptions=0)", batchsize=100000)
writeTargetsout(x=args, file="targets_PEtrim.txt", overwrite=TRUE)
FASTQ quality report
The following seeFastq and seeFastqPlot functions generate and plot a series of
useful quality statistics for a set of FASTQ files including per cycle quality box
plots, base proportions, base-level quality trends, relative k-mer
diversity, length and occurrence distribution of reads, number of reads
above quality cutoffs and mean quality distribution. The results are
written to a PDF file named fastqReport.pdf.
args <- systemArgs(sysma="param/tophat.param", mytargets="targets.txt")
fqlist <- seeFastq(fastq=infile1(args), batchsize=100000, klength=8)
pdf("./results/fastqReport.pdf", height=18, width=4*length(fqlist))
seeFastqPlot(fqlist)
dev.off()
Figure 1: FASTQ quality report for 18 samples