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myles-lewis / locuszoomr

A pure R implementation of locuszoom for plotting genetic data at genomic loci accompanied by gene annotations.
GNU General Public License v3.0
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Can non-modal species use locuszoomr #24

Closed yunmika closed 3 months ago

yunmika commented 3 months ago

Thanks for the work you've done on locuszoomr, it's been very helpful, but I was wondering if it could be applied to non-modal species?

yunmika commented 3 months ago

I'm trying to build the ens_db, but every time it fails at this step, so I'm trying to understand if I have to use the ens_db with the species already built in order to use locuszoomr?

myles-lewis commented 3 months ago

Hi Fuchuan Han,

Yes locuszoomr should work with non-model species but you must have a functional ensembldb object for the package to work. I’ve not generated a fresh ensembldb object myself so I can’t really help with that process. Have you checked AnnotationHub, to see if your species of interest already had a genome reference db available?

Bw, Myles

yunmika commented 3 months ago

Thank you for your reply. I did stop at the step of building ens_db, which is more demanding on the gff file. This should be the main reason that prevents the use of locuszoomr without ens_db species. I will make some other attempts.