adding a custom genome

[Timothy Russell]

Hi,

I have read the webpage that describes creating sessions and custom sessions very thoroughly, and I can't find any option that describes how to upload a genome that is not supplied as part of the base choices in the 'genome' tab. Am I missing something or is there no option to do so?

Thanks!

[Daniel Schmelter]

Hello Timothy,

Thank you for using the Genome Browser and asking about visualizing a custom genome assembly.

While we have more than 200 native genome assemblies, you are not limited to genomes that we host natively on our website. You can visualize any sequence you want using our Assembly Hubs feature. Before making your own, you may want to double-check whether your assembly is listed by searching the species name or the GCF ID from our Genomes page, which was recently updated to include public assembly hubs:

https://genome.ucsc.edu/cgi-bin/hgGateway

You can read more about creating your own Assembly Hub in the following resources and follow the examples to understand the process of visualizing a custom reference genome:

http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly
http://genomewiki.ucsc.edu/index.php/Assembly_Hubs
http://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html

The basic process requires converting the organism's Fasta file into a 2bit file and arranging your data in a web-hosted location along with configuration lines. Once you have your web directory, data files, and configuration file(s), you will need to enter the URL to your hub.txt configuration file into the My Hubs page. You should then see your data visualized on the Genome Browser along with any custom annotation files that you included.

I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genome Browser

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