Please note the arguments you can use in a track line
for a type=wiggle_0 format file:

http://genome.ucsc.edu/goldenPath/help/wiggle.html

The arguments useScore, scoreMin, scoreMax have no meaning
with a wiggle track.  A wiggle track does not display items
in a gray-scale fashion, it draws a graph of the data values.

--Hiram

----- Original Message -----
From: "Liz Ashley" <lizzi...@hotmail.com>
To: won...@gmail.com
Cc: galaxy-user@lists.bx.psu.edu
Sent: Friday, May 11, 2012 6:05:14 AM
Subject: Re: [galaxy-user] Displaying bed files in ucsc



In the title information you need to include UseScore information including the 
range you want to cover with your histogram. There is a section in the UCSC 
website that explains the content: 
http://genome.ucsc.edu/FAQ/FAQformat.html#format1 

For stating the range of your histogram: scoreMin=X scoreMax=X. This will mean 
that the greyscale shading uses the two X values as the value for white and 
black, all other points will be an even range like the example on the UCSC 
browser page. 

When I was doing this the information I used was wiggle format: 
track type = wiggle_0 name="name of track" description="description" useScore=1 
scoreMin=0 scoreMax=6. 
ChrNo StartPos FinishPos Score 

Hope that makes sense/helps 
lizzy 












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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