GBIB - Mirror Tracks & Default Tracks

[Gokhul Krishna Kilaru]

Dear UCSC Browser Team/GBIB Team,

Hope all is well in the wild west.

I have downloaded GBIB and packed it inside a virtualbox. Everything seems to be perfect. I have a few questions.

1. If I want to mirror the mm10 tracks only(by download), how much space am I looking at? I plan on buying a 500GB SSD. Will that be sufficient?

2. How do I change the default tracks that appear on the browser? I only want to show the UCSC & Gencode mm10/M14 tracks.

Please let me know.

Thanks

~Gokhul

[Cath Tyner]

Hello Gokhul,

Thank you for contacting the UCSC Genome Browser support team. From your GBiB, you can find the total size of tracks for mm10 here:

../cgi-bin/hgMirror?clade=mammal&org=Mouse&db=0

To change the default tracks that appear on the browser, click on the "hide all" button under the tracks graphic, and then change the visibility for the UCSC Genes and the GENCODE tracks to "full" and "show", respectively. For more information, see the "Annotation track display modes" section on the tracks help guide: https://genome.ucsc.edu/goldenpath/help/hgTracksHelp.html#FineTuning

To reset to default tracks, you can click the "default tracks" button under the browser tracks graphic. 

If you are new to the UCSC Genome Browser, you might also be interested in some introductory tutorials:

UCSC Genome Browser - Training

http://genome.ucsc.edu/training/index.html

UCSC Genome Browser Tutorials by OpenHelix:

http://www.openhelix.com/ucsc

UCSC Genome Browser Videos:

https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos

Please respond to this list if you have further questions!

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Enjoy,

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Gokhul Krishna Kilaru]

Hi Cath-

Thank you for the info. Seems like we need at least 1TB for things to settle comfortably.

Regarding the default tracks - I am aware of the "hide all" function. But what I want to do is hide them all by default instead of visiting the browser, hiding them and then opening my tracks of choice. Any way to do this?

Appreciate your time in this regard.

Cheers

~G~

[Jairo Navarro Gonzalez]

Dear Gokhul,

Thank you for using the UCSC Genome Browser and your question about hiding tracks by default in GBiB. 
To display only the UCSC & Gencode mm10/M14 tracks, you will have to create a local trackDb database for mm10 and edit the hg.conf.local file to use your local trackDb database.

Create a trackDb_local database

You would first have to create a trackDb_local database table for mm10 using special commands.
You can learn more about creating this database from the following trackDb help page:

http://genome.ucsc.edu/goldenPath/help/mirrorManual.html#adding-tracks-to-the-browser

Edit hg.conf.local

Once you have created your trackDb_local database, you can edit hg.conf.local to point GBiB to your local database. The hg.conf.local file can be found in the following GBiB directory:

/usr/local/apache/cgi-bin/

We are currently working on an alternative to creating the trackDb_local database, but we do not have set completion date. If you would like email updates about the UCSC Genome Browser, you can subscribe to our Announcements List:

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Jairo Navarro 
UCSC Genomics Institute

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