Good Evening Jose:

Please note the types of graphing formats you can display at UCSC:
   http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format

I would recommend converting your bedgraph file to a bigWig file and display
that via a remote URL.  This would be your most efficient mechanism of display.

--Hiram

----- Original Message -----
From: "Xianrong Wong" <won...@gmail.com>
To: "James Robinson" <jrobi...@broadinstitute.org>
Cc: galaxy-user@lists.bx.psu.edu
Sent: Thursday, May 10, 2012 9:27:07 PM
Subject: Re: [galaxy-user] Displaying bed files in ucsc


I changed it to bedgraph and can no longer view in UCSC (the button to view in 
UCSC was not there anymore). I had it in bed format subsequently and put in a 
header. I was looking at the bedgraph/wiggle header documentation on UCSC but 
don't find any that describes displaying scores in histogram format. I saw that 
we can change colour the intensity of the bars based on scores though. 

Jose 


On Thu, May 10, 2012 at 10:27 PM, James Robinson < jrobi...@broadinstitute.org 
> wrote: 


Hi Jose, 


What you have described is a "bedgraph" file. Perhaps changing the file 
extension to "bedgraph" will be enough, if not you might be required to enter a 
track line. See UCSC for details. 



On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong < won...@gmail.com > wrote: 



Hello, I have a bed file in this format: chr# start end scores. I tried to view 
it in ucsc main but it showed only where the fragments are(based on the start 
and end coordinates) with numerical scores beside each fragment. How do I view 
the file as a histogram format? What format will I need to convert the file to 
and where can I do the conversion? Any advise is greatly appreciated! 

Jose 
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