Bioinformatics Inquiry regarding Registered Genomes

[Kelso Cochran]

To whom it may concern,

I'm a researcher working in the Macias-Muñoz Lab at UCSC (EEB) and I have a bit of a bioinformatics question regarding the genome browser. To preface, I've been learning bioinformatics independently for only a couple months so I apologize for my limited understanding but I'd appreciate any guidance in navigating this current roadblock if possible.

I'm trying to utilize an R package called BSgenomeforge to create a BSgenome file that can be utilized in another pipeline. With that context, the package utilizes the command: 'forgeBSgenomeDataPkgFromUCSC()' which is limited in that it can only retrieve genomes "registered" in the UCSC genome browser. 

My questions are: How does a genome become "registered" in the UCSC Genome Browser & how might it be different from a genome that is just viewable from the browser?

This specifically regards a Hydra vulgaris AEP genome (HydraT2T_AEP; GCF_038396675.1 / NCBI) that I'm able to view through the browser but isn't included in the list of registered genomes. For reference, I've also attached a text file below containing the list of ~96 genomes output by the BSgenomeForge command 'registered_UCSC_genomes()'

Additionally, I'm aware the BSgenome/BSgenomeforge package is managed independently so I understand if this list is similarly not determined by UCSC but I'm unable to find any information illustrating otherwise and figured I'd ask.

Thank you very much for your time, I'm grateful for any help you can offer or direction you can point me toward clarifying my issue. Let me know if there's any additional information I can provide. 

Best regards,

Kelso N. Cochran

(she/they)

Asst. Specialist | Macias-Muñoz CnidoLab 🪼

Ecology & Evolutionary Biology | UC Santa Cruz

Coastal Biology Building, Rm 277 | cell: 760-834-5819

[Maximilian Haeussler]

Hi Kelso,

Thanks for reaching out. We changed the way how we add genomes to the genome browser a few years ago, because there are so many these days. Can you "open a ticket" or email the authors of this package and CC us, and explain your problem? Then we can sort this out with them and you can test the fix. The fix should be really simple, we have a new API call to get all the genomes, they may be using a different mechanism, without their input, this will be very hard to us to resolve.

I think the main maintainer is Herve Pages (we communicated with him before about other issues), but the recommended way to ask them is via opening a ticket here: https://github.com/Bioconductor/BSgenomeForge/issues

thanks

Max

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAGv%2BH%2BJphKLw2gGZwOerx4MisBL2vp0_n4iRZ34MTOOXJDLvGg%40mail.gmail.com.