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.