I really like the features that are provided in karyoploteR.
But, I am working with different organisms. I am able to find the organisms of interest using:
My organisms of interest is Arabdidopsis lyrata and I installed it using.
But, when I try to plot the genome I get error message.
karyoploteR::plotKaryotype(genome = "BSgenome.Alyrata.JGI.v1")
Error in .getInstalledPkgnameFromProviderVersion(genome, masked = masked) :
Couldn't find a BSgenome data package that matches genome assembly
(a.k.a. provider version): Alyrata.JGI.v1
Please use 'available.genomes()' (or 'available.genomes(type="source")')
to check the list of BSgenome data packages that are available in the
Bioconductor repositories for your version of R/Bioconductor.
If you don't find what you are looking for, please see the BSgenomeForge
vignette in the BSgenome software package for how to forge a BSgenome
data package for your organism of interest.
But, I am not able to load this genome. I have tried using different genome names like `Alyr`, `Alv1` and also tried looking what acronym is set for lyrata. But I can't find it.
Another question: How do I plot the karyotype if I don't have a BsGenome but a GTF, GFF file.