In Silico PCR Drop Down

[Brandi Cantarel]

I have added a number of novel genomes to my UCSC genome browser mirror.  When I try the In-Silico PCR tool — I get the “Note”

In-Silico PCR is not available for Asian elephant Asiatic elephant (mEleMax1 primary hap 2022); defaulting to Human Jan. 2022 (T2T CHM13v2.0/hs1)

It seems the drop down for this tool doesn’t contain any of the organism that I added to the browser.  How can I add these “other” genomes so that they show up in the drop-down?

Thanks!

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You will have to set up your own gfServer to have BLAT service for your custom genome assemblies. These configurations are set in the hgcentral tables for your mirror:

https://genomewiki.ucsc.edu/index.php?title=Browser_Installation#Set_up_the_%22hgcentral%22_tables

You can learn more about configuring the gfServers from the following wiki page:

https://genomewiki.ucsc.edu/index.php/Running_your_own_gfServer

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

I am happy to let you know that the GCF_024166365.1 assembly is also available as a GenArk assembly hub:

https://genome.ucsc.edu/h/GCF_024166365.1

Using this GenArk hub is an alternative to creating a mirror for your custom genome assemblies. If you need an assembly that is not on the GenArk system, please let us know, and we can create the assembly hub with a working BLAT service.

Search GenArk:

https://hgdownload.soe.ucsc.edu/hubs/

Request an assembly:

https://genome.ucsc.edu/assemblyRequest.html

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser