TEQC - new version Bioc - problem with IRanges
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msourdeix • 0
@msourdeix-16155
Last seen 4.2 years ago

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.

teqc iranges • 621 views
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m.hummel ▴ 10
@mhummel-8646
Last seen 4.1 years ago
Germany

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.

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