[Genome] Fwd: Genome graph window size

[Galt Barber]

Put your input data in a local file or make it accessible via URL.

In Genome Graphs,
after clicking upload and selecting your input, give it
at least a name for the data set.
Click submit.
If you see no errors,
You should be returned to the main Genome Graphs view.

Look in the drop down list for the name you gave your
dataset and select that.  It should render your graph.
This is considered a Genome-Graphs custom track,
and it's not the same as a regular custom track.
(Although a regular custom track could be imported
into Genome Graphs, it would be done with 10,000 bp windowing.)

When you click on your genome graph, it should jump
to a genome-browser view of the same region, and from
there you can continue to zoom etc.

-Galt


On Thu, 10 Jan 2008, Robert Darnell wrote:

> Hi Galt:
>
> Thanks for the help.  I sent the email below back to Hiram, from which
> you can see I am in dire straits.
>
> Your solution looks interesting...and makes me wonder if I am
> inputting my data in the wrong format?  When I try loading the file
> format the way you suggested I get errors loading through custom
> tracks (Error File 'test2.txt' - Error line 2 of custom track:
> chromStart after chromEnd (100000000 > 200)), and importing directly
> into Genome Graph it seems to load but is lost (to me)...
>
> Bob
> _________________________________
> Robert B. Darnell
> The Rockefeller University
>
>
> Begin forwarded message:
>
> > From: Robert Darnell <darnelr at rockefeller.edu>
> > Date: January 10, 2008 2:21:30 PM EST
> > To: Hiram Clawson <hiram at soe.ucsc.edu>
> > Subject: Re: [Genome] Genome graph window size
> >
> > Hi Hiram:
> >
> > Thanks very much for the help.  I am going to try your wiggle idea.
> > In the meantime, can I ask an even more basic question about Genome
> > Graph.  The BED files I am plotting look great, but I realize the Y
> > axis doesn't bear any relationship to the data that I can figure
> > out.  So, I made a few test files, which only serve to convince me
> > further I have no idea what I am plotting on Y:
> > track name='test data' description='test data'
> > chr10 101168028 101168069 4.88
> > chr10 101230425 101230508 7.23
> > chr9 10000000010000010025
> >
> >
> > and
> >
> > track name='test data' description='test data'
> > chr9 100000000	100000100	200
> >
> >
> > I do understand that the Y axis is plotting 1/3 and 2/3 of
> > something, but it seems to be a fraction of the number 0.01, not of
> > my data...
> >
> > Thanks for the hand-holding!
> >
> > Bob
> > _________________________________
> > Robert B. Darnell
> > The Rockefeller University
> >
> >
> > On Jan 10, 2008, at 1:46 PM, Hiram Clawson wrote:
> >
> >> Good Morning Robert:
> >>
> >> If your data can be calculated to a consistent window size,
> >> say one data point for every 100bp, you can use the
> >> wiggle format to view the data in the genome browser:
> >> http://genome.ucsc.edu/goldenPath/help/wiggle.html
> >>
> >> The genome graphs are whole genome viewpoints and wouldn't
> >> be able to show your data detail below a couple 100 thousand
> >> bases.  Unless you view them in the genome browser, where
> >> you could instead view them as wiggle data plots.
> >>
> >> Wiggle data points are bar graphs at the specified
> >> locations with the bars of size "span".  (span must
> >> be consistent)  Whereas, the genome graph data
> >> points are points on a line graph.  They are different
> >> types of graphs.  The wiggle data can be fudged into
> >> looking like a line graph by setting the graph
> >> options to "points" (actually the lines of the tops
> >> of the bars) and set smoothing on to smear those little
> >> line segments into a continuous looking line.
> >>
> >> --Hiram
> >>
> >> Robert Darnell wrote:
> >>> Hi:
> >>> I'm a molecular biologist (so have mercy please) interested in
> >>> trying  to graph BED files uploaded into Genome Graphs, but to
> >>> have the data  plotted in a narrower window than 10,000bp; even
> >>> 1,000 bp would be an  improvement I think for our data, or,
> >>> optimally, 100bp.  Is this  impossible because of computation
> >>> time, or feasible?
> >>> Thanks,
> >>> Bob
> >>> _________________________________
> >>> Robert B. Darnell
> >>> The Rockefeller University
> >>> _______________________________________________
> >>> Genome maillist  -  Genome at soe.ucsc.edu
> >>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> >>
> >
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>