Creating a hub for Rice (Oryza sativa)

[yuliya karpievitch]

Hi, 

I would like to add a hub for Rice to the UCSC browser, I tried to do so via Session but that defaulted to Arabidopsis that I was using earlier. 

I have genes.gtf file for the IRGSP-1.0 genome assembly. Can you please let me know how I can add the Rice? I am hoping that is possible as there are a few hubs for plants already. 

Many thanks in advance!

Yuliya

 

[Brian Lee]

Dear Yuliya,

Thank you for using the UCSC Genome Browser and your question about creating a hub for Japonica rice Oryza sativa IRGSP-1.0.

It may be of help to review our hub documentation, http://hgwdev.cse.ucsc.edu/goldenPath/help/hgTrackHubHelp.html, to better understand how hubs work. Hubs are remote hosting of binary files, with principally three text files, that the browser accesses quickly to display researcher's annotations. Searching our archived mailing list answers can provide helpful hints, such as this introduction to hubs: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/trackDb.txt$20genomes.txt$20brianlee/genome/mUH5GtWXWaw/AVrt7hGy7dcJ

Your question is specific to assembly hubs, which are hubs for genomes that are not hosted by UCSC. If you are going to build an assembly hub, please review our Assembly Hubs Wiki: http://genomewiki.ucsc.edu/index.php/Assembly_Hubs

Once you have reviewed this information about hubs, you might be interested to learn that a pre-existing assembly hub has been created for Japonica rice, Oryza sativa IRGSP-1.0, along with many other plant assembly hubs: http://genome-test.cse.ucsc.edu/gbdb/hubs/genbank/plant/plant.ncbi.html

Please review the entire NOTE at the top of that page about how the work is a prototype in progress. If you search for IRGSP-1.0 on that page you will find an entry where you can click the "Japonica rice" link and end up on our development site with the hub selected: http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.cse.ucsc.edu/gbdb/hubs/genbank/plant/hub.ncbi.txt&genome=GCA_001433935.1_IRGSP-1.0&position=lastDbPos

Before clicking "Go" to load the hub, please review the notes displayed that will describe where the files for this assembly hub is located in case you wish to copy them and locally load and use them and the top "WARNING:" about how you are accessing the UCSC Genome Browser development site where data and software can change.

If you wanted to display your information on this assembly hub, you could click the My Data column and then Custom Tracks and paste data formatted to display such as this example track from the hub:

track type=bigBed name=MyData description="Data I host that I want to display on this Assembly Hub" bigDataUrl=http://genome-test.cse.ucsc.edu/gbdb/hubs/genbank/plant/GCA_001433935.1_IRGSP-1.0/bbi/GCA_001433935.1_IRGSP-1.0.ncbiGene.ncbi.bb

Here is a session to the hub with such a custom track: http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hub_1551_GCA_001433935.1_IRGSP%2D1.0.customTrack

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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