[Genome] Fwd: Genome graph window size

[Robert Darnell]

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
>>
>