Question: TEQC - new version Bioc - problem with IRanges
0
gravatar for msourdeix
15 months ago by
msourdeix0
msourdeix0 wrote:

Hi everyone,

I have a problem when working with TEQC. I retrieve a targets and a reads object like this :

targets <- get.targets(targetsfile=bed, chrcol=1, startcol=2, endcol=3, skip=0)

reads <- get.reads(args[i], filetype="bam")

With no problem. Then I launch

Coverage <- coverage.target(reads, targets, perTarget=T, perBase=T)

And this tells me

Error in .check_arg_names(width, "width", x_names, x_names.label) :
  when 'width' has names, they must be identical to 'seqlevels(x)'

I recently updated my OS and installed R and Bioconductor more recent versions. Today I have TEQC 4.2, R 3.5 and Bioconductor 3.7.

It used to work perfectly with TEQC 3.16, R 3.4 and Bioconductor 3.6.

Could you please help me ??

Thanks a lot.

iranges teqc • 320 views
ADD COMMENTlink modified 15 months ago by m.hummel10 • written 15 months ago by msourdeix0
Answer: TEQC - new version Bioc - problem with IRanges
0
gravatar for m.hummel
15 months ago by
m.hummel10
Germany
m.hummel10 wrote:

Thank you for pointing this out. The problem is most probably related to chromosomes in the bam file without any mapped reads. I have changed get.reads() in order to remove those chromosomes (seqlevels) from the resulting GRanges object. This fix should be available soon in the development version of TEQC.

ADD COMMENTlink written 15 months ago by m.hummel10
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