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" <lizzilou@hotmail.com>
To: wongxr@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 < wongxr@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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___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/