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PostPosted: Mon Jul 29, 2013 12:56 pm 
To Bejerano Lab,

I am confused. I've downloaded and install the GREAT Source Code [http://bejerano.stanford.edu/help/display/GREAT/Download]. It runs without errors, however, I don't see any ontology results. I only get p-values. Am I missing something?
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PostPosted: Sun Aug 04, 2013 4:06 pm 
Site Admin
Hi Raymond,

The GREAT source code includes the tools to define gene regulatory domains and to calculate the enrichment statistics. The ontology data is not included since all of the data can be downloaded from the original sources. Please see http://bejerano.stanford.edu/help/display/GREAT/Ontologies for links to the various public sources and download the ones that are relevant for your work.

Thanks,
Bejerano Team
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PostPosted: Fri Aug 30, 2013 7:53 am 
Hi,

Is there a way to download ALL ontologies at once? I.e. would it be possible to zip a file of all the data here http://bejerano.stanford.edu/help/display/GREAT/Ontologies?

We wish to install the tool, and it would save us a lot of time if we can avoid the manual downloading.

Thanks much!
Alon.
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PostPosted: Sun Sep 01, 2013 6:57 am 
Site Admin
Hi Alon,

We have not created a downloadable package of all the ontology data.

Thanks,
Bejerano Team
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PostPosted: Sun Sep 01, 2013 7:28 am 
OK, we will try to work with what you have.

If you do get to pool all the ontology data to one directory, please let us know.

Thanks,

Alon.
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PostPosted: Sun Sep 01, 2013 7:33 am 
Site Admin
Will do. Also consider if the programming interface - http://bejerano.stanford.edu/help/display/GREAT/Programming+Interface will be sufficient for your work without reimplementing GREAT.

The programming interface will allow you to batch jobs and retrieve the results as tsv files.

Thanks,
Bejerano Team
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PostPosted: Sun Sep 01, 2013 7:40 am 
Hi -

Thanks for the quick reply.
I have tried the programming interface, but I assume that running the code on our servers would be much more efficient, and can reduce the load from your servers.

Best,
Alon.
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