I am using TEQC for analysis of my paired-end bam files.
If I use
pairedend = TRUE in the following:
TEQCreport(sampleName = "", targetsName = "", referenceName = "", destDir = "TEQCreport", reads = get.reads(), targets = get.targets(), pairedend = TRUE, genomesize= 12345678, k=c(1, 2, 3, 5, 10, 20), covthreshold = 8, CovUniformityPlot = TRUE, CovTargetLengthPlot = TRUE, CovGCPlot = TRUE, duplicatesPlot = TRUE, figureFormat = c("jpeg", "png", "tiff"))
1) Is it equivalent to the following three commands or I have to remove
singleReads separately for all my bam files?:
reads <- get.reads("myBAM.bam", filetype="bam") readpairs <- reads2pairs(reads) reads <- reads[!(reads$ID %in% readpairs$singleReads$ID), , drop=TRUE]
2) If yes, then the parameters mentioned below would consider only readpairs (no single reads)?
CovUniformityPlot = TRUE, CovTargetLengthPlot = TRUE, CovGCPlot = TRUE, duplicatesPlot = TRUE
3) If no, how can I incorporate those three commands in
Kindly guide. Thanks!