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bernatgel / karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
https://bernatgel.github.io/karyoploter_tutorial/
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BSgenomeForge new rat genome #106

Open motutaj opened 3 years ago

motutaj commented 3 years ago

Hi Bernat,

Thank you for the great tool. I would like to create the karyotype for a new rat genome mRatBN7.2/rn7 - NCBI released Nov 2020 but UCSC just recently: http://hgdownload.soe.ucsc.edu/goldenPath/rn7/bigZips/rn7.2bit . Could you please add it to the list of registered assemblies (GCA_015227675.2)?

Many thanks, Monika

bernatgel commented 2 years ago

Hi @motutaj

If the genome is in UCSC, in theory, you should be able to work with it simply specifying genome="rn7". It will instruct you to install the corresponding BSgenome and automatically try to download the cytobands from UCSC. The problem is that a bug in another package is preventing it from downloading them, so it will fail.

I've tried to download the cytobands and add them to the mini-database of genomes and cytobands in karyoploteR, but seems like UCSC does not have them. They are all "gneg" and with no names.

I try to add only genome assemblies with the complete information (as rn6) and for genomes such "rn7" I'd recommend using a custom genome if you want to use it.

Does it make sense?

Bernat