[Genome] Question about extending genome graph (/cgi-bin/hgGenome) parameters

[Robert Kuhn]

Hello, Ross,

We're glad you like the Genome Graphs tool.  We will take your segguestions
to heart and see if we can implement them.

Bet wishes,

			--b0b kuhn
			ucsc genome bioinformatics group


> From genome-bounces at soe.ucsc.edu  Mon Oct  8 02:17:48 2007
> To: genome at soe.ucsc.edu
> Cc: ross.lazarus at channing.harvard.edu
> Subject: [Genome] Question about extending genome graph (/cgi-bin/hgGenome)
> 	parameters
> 
> Genome Graphs is a great way to see multiple custom tracks. I'm using it on an 
> internal private mirror here at the Channing lab to display hundreds of outputs 
> from analyses of large association studies for the investigators.
> 
> I have a proposal that would make it even greater with a relatively small 
> increase in complexity. I have a working Galaxy genome graphs datatype that 
> works exactly like the current Galaxy bed file viewer - it has a "view at ucsc" 
> link that opens a (in our case!) local mirror genome graphs display. Users 
> really like it, but they complain about 3 things - the lines joining points are 
> misleading for these statistics; they don't like the fact that the default is 
> all tracks on at 30 pixels or so; and they want the tracks scaled sensibly.
> 
> I was wondering if we could have some additional parameters - eg 1) a flag to 
> substitute bars when you don't want the apparent smoothing of joined dots, and 
> 2) some ways to hint at each track's vertical size 3) and scale, 4) and default 
> state (full, packed etc)? I am constructing the URL in python code and it's easy 
> for me to comply with extensions to the current genome graphs call to 
> /cgi-bin/hgGenome
> 
> I quickly understood from reading the code that making these changes correctly 
> would be a non trivial, high risk venture for me. Does anyone with deep 
> knowledge have time for this please? I would be interested in discussing the 
> possibility of supporting this work via a small (!) subcontract from one of my 
> grants if that is a realistic option and would help get this done ?
> 
> 
> > From ann at soe.ucsc.edu  Mon Feb  5 05:42:17 2007
> > From: ann at soe.ucsc.edu (Ann Zweig)
> > Date: Mon, 05 Feb 2007 07:42:17 -0600
> > Subject: [Genome-announce] New Genome Graphs Tool Available in Genome Browser
> > Message-ID: <45C73439.6090804 at soe.ucsc.edu>
> > 
> > We are pleased to announce the release of a new software tool in the 
> > Genome Browser collection, the Genome Graphs tool. Genome Graphs offers 
> > the ability to upload and display genome-wide data sets such as the 
> > results of genome-wide SNP association studies, linkage studies and 
> > homozygosity mapping. The Genome Graphs tool may be accessed from the 
> > menu on the UCSC Genome Bioinformatics home page, or from this link: 
> > http://genome.ucsc.edu/cgi-bin/hgGenome
> > 
> > The initial release of Genome Graphs includes the following features:
> > 
> > - upload several sets of genome-wide data and display them simultaneously
> > - click on an area of interest and go directly to the genome browser at 
> > that position
> > - set a significance threshold for your data and view only regions that 
> > meet that threshold
> > - view the genes that exist in areas where your data meet your 
> > significance threshold
> > 
> > For more information about the Genome Graphs tool, visit the Gateway 
> > page or consult the Getting Started on Genome Graphs section in the 
> > User's Guide: 
> > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GenomeGraphs
> > 
> > Genome Graphs was written by Jim Kent of the UCSC Genome Bioinformatics 
> > Group.
> > 
> > -------
> > Regards,
> > Ann Zweig
> 
> 
> 
> -- 
> Ross Lazarus MBBS MPH, Director of Bioinformatics
> Channing Laboratory, 181 Longwood Ave., Boston MA 02115, USA.
> Tel: +617 525 2730  Fax: +617 525 0958
> 
> 
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