Bat Genomes

[Roger Long]

Where can I find the complete stand-alone genomes for Myotis davidii, Eptesicus fuscus, and Pteropus alecto. They are part of the 99-way alignment, but I cannot find the individual genomes.

Thanks,

Roger

[Matthew Speir]

Hi Roger,

Thank you for your question about finding these different bat genomes in the UCSC Genome Browser. These genomes are available on our preview server as:

• David's myotis (bat) (Myotis davidii): http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=myoDav1
  
• Big brown bat (Eptesicus fuscus): http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=eptFus1
  
• Black flying-fox (Pteropus alecto): http://genome-preview.ucsc.edu/cgi-bin/hgGateway?db=pteAle1

You can also find minimal downloads for these species on our preview download server at:

• http://hgdownload-test.soe.ucsc.edu/goldenPath/myoDav1/
• http://hgdownload-test.soe.ucsc.edu/goldenPath/eptFus1/
• http://hgdownload-test.soe.ucsc.edu/goldenPath/pteAle1/

Any data on the preview server is still under development and subject to change at any time. If you decide to use these data, please do so with caution.

You are also welcome to create assembly hubs for all of these species. Our assembly hub feature allows users to host their genome and related annotations on a publicly-accessible web server and then visualize these within our browser. You can find information about creating assembly hubs on the following help pages:

• http://genomewiki.ucsc.edu/index.php/Assembly_Hubs
• http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
  

Please review this previously answered mailing list question for additional information on creating and maintaining assembly hubs:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/ozSm1vjaxRY/yZNRpWHRcvQJ

If you do create an assembly hub containing these species and host the data, we can add it to our public hubs page along side other externally hosted hubs: http://genome.ucsc.edu/cgi-bin/hgHubConnect?

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.

Matthew Speir
UCSC Genome Bioinformatics Group

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