Unlisted Organisms in the Genome Browser

[Aakash Sur]

Hi, 

 I want to study a genome not in the website database. What should I do?

Best, 

--

Aakash Sur

Biomedical and Health Informatics | School of Medicine
University of Washington

[Brian Lee]

Dear Aakash,

Thank you for using the UCSC Genome Browser and your question about how to study a genome not on the website.

One option is to use a UCSC Assembly Track Hub. Assembly Track Hubs allow users to take advantage of remote servers to send information to the Browser and view both genomes and annotations on external genomes. Researchers can build these Assembly Hubs on their own, or use ones already built and hosted by others.

--Existing Assembly Hubs--

On our public hubs page, http://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs, you can find some assemblies other consortiums or research groups have built, such as a "C.elegans wild isolate assembly hub" where not only have external genomes been built, but also many layers of annotation have been provided.

Another location where you can find thousands of Assembly Hubs automatically generated from Genbank files are the following prototype site, http://genome-test.cse.ucsc.edu/gbdb/hubs/genbank/vertebrate_other/vertebrate_other.ncbi.html, where you can select different categories such as "vertebrate other" and view a list of 156 assemblies hubs and click links such as "canary" or "Vipera berus berus" to take you to the related bird or snake Assembly Hub.

--Creating Your Own Assembly Hubs--

When you connect to one of the Genbank hubs, on the welcome gateway page you will find a "To download this data..." section that will provide steps on how you can pull the Assembly Hub to your own remote server location where you could edit it and make it your own.

Similarly at this related Assembly Hub Quick Start page, http://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html, you can pull a basic example Assembly Hub and edit it to make it your own.

To make one of these example Assembly Hubs your own, you would swap in a new "2bit" file that describes your assembly. By starting with a fasta file for your genome (your.fasta) you would use the tool faToTwoBit (available here http://hgdownload.soe.ucsc.edu/admin/exe/) and the command "faToTwoBit your.fasta your.2bit" to build the 2bit. You can see some example steps of using the Quick Start Assembly Huband swapping out the files here: https://github.com/ucsc-browser/assemblyHubEx

If you wish to build an Assembly Hub, please see our Assembly Hub wikipage, http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

I also recommend this PDF from at talk that discusses the structure of custom tracks, track hubs, and assembly hubs: http://genomewiki.ucsc.edu/images/0/04/AssemblyHubsUCSC.pdf

--Hosting Assembly Hub Data--

Some people have trouble finding a remote server to host the data files that are used in Assembly Hubs, as they require byte-range requests and free data storage sites like DropBox or Google Drive do not support those requests since it could allow pirated video content to stream. The NSF funded site Cyverse, https://de.cyverse.org/, can be one solution for scientists looking for free data storage if your own university or institution does not provide you with an internet accessible location to store your data.

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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