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A.Singh
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@asingh-22624
Last seen 3.5 years ago
I am trying to generate QC report for my ChIP-seq bam files using qQCreport module of QuasR. My files are aligned, sorted and indexed.
It shows error: Error in .normarg_totalsize(totalsize) : 'totalsize' must be a single integer
My code is pasted below:
> library(QuasR)
> library(BSgenome)
> library(Rsamtools)
> library(rtracklayer)
> library(GenomicFeatures)
> genomeFile <- "genome.fa"
> genomeFile
[1] "genome.fa"
> sampleFile <- "ChIP.txt"
> proj1 <- qAlign(sampleFile, genomeFile, paired="no")
Creating .fai file for: D:/genome.fa
all necessary alignment files found
> qQCReport(proj1, pdfFilename="qc_report.pdf")
collecting quality control data
Error in .normarg_totalsize(totalsize) :
'totalsize' must be a single integer
Any suggestions are much appreciated.
Thank you
We have not seen that kind of error before. The error message is not from QuasR, it might be from IRanges.
Do you know if all your bam files contain valid alignments? You could test with: alignmentStats(proj1)
Alternatively, do you have a minimal, reproducible example (maybe a single bam file with only a small subset of your data) that you could share, so we can look further into the problem?
Thank you, Michael
Hi Just double checking: is the genome you provide to generate the qProject (i.e. "genome.fa" ) the same genome which has been used to originally generate the bam files ?
Regards, Hans-Rudolf