Question: TEQC (Target Enrichment Quality Control, R package) : Clarification on paired-end reads
0
gravatar for bioinfo8
3.7 years ago by
bioinfo8130
bioinfo8130 wrote:

Hi,

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 TEQCreport()?

Kindly guide. Thanks!

teqc bioconductor ngs R paired-end • 825 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by bioinfo8130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1434 users visited in the last hour
_