Request for Guidance on Adding Custom Reference Genome to UCSC Genome Browser

[Areta Krisar]

Dear UCSC Genome Browser Group,

My name is Areta, and I am currently an undergraduate student in my final year, working on my thesis. I am writing to seek guidance regarding the use of custom tracks in the UCSC Genome Browser.

At present, the reference genome required for my research is not available in the database, and I need to incorporate my own reference genome. Although I have attempted to follow available instructions, including guidance from AI tools, I am still experiencing difficulties in properly adding and visualizing my custom reference.

I would greatly appreciate it if you could provide any tutorials, documentation, or recommended resources, such as instructional videos, that could help me better understand the process.

Thank you very much for your time and assistance. I look forward to your response.

Sincerely,

Areta

[Matthew Speir]

Hello, Areta.

Thank you for your question about loading a custom assembly in the UCSC Genome Browser and good luck on your undergraduate senior thesis.

We provide a quick start assembly hub here: https://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html. With this, you should only need to modify some values to point to your local file paths. Our assembly hub user guide, https://genome.ucsc.edu/goldenPath/help/assemblyHubHelp.html, contains specifics about the various settings for configuring your hub.

Can you provide more details about where in the process you're getting stuck? If so, we can try to provide more specific help.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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