Question: Error running the addCoverage command in QSEA with a custom BSGenome reference
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4 months ago by
apt.university0 wrote:


I am trying to run the following command: 

qseaSet=addCoverage(qseaSet, uniquePos=TRUE, paired=TRUE)

but I keep on getting the error below.

I am running version sea_1.6.0 and running on a custom BSGenome reference. Any suggestions are greatly appreciated.


Reading bam alignment combined_bams/S4_Apo1_ALL_sorted.bam

Number of imported sequencing fragments: 13908900

Calculating short read coverage for genome wide windows.

Error in data.frame(seqnames = ReadsL[[idx]]$rname[keep], start = pos[keep] +  :

  arguments imply differing number of rows: 0, 1

In addition: Warning messages:

1: In min(isize) : no non-missing arguments to min; returning Inf

2: In max(isize) : no non-missing arguments to max; returning -Inf
ADD COMMENTlink modified 4 months ago by Matthias Lienhard140 • written 4 months ago by apt.university0
gravatar for Matthias Lienhard
4 months ago by
Max Planck Institute for molecular Genetics, Berlin, Germany
Matthias Lienhard140 wrote:


this is due to a bug, resulting in the error message if a chromosome/conting is included that does not contain any valid alignment. It is fixed in qsea version 1.7.1.

As a workaround you could also exclude chromosomes without alignments from the parameter.

Best, Matthias


ADD COMMENTlink written 4 months ago by Matthias Lienhard140
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