Re: [galaxy-user] Displaying bed files in ucsc

2012-05-11 Thread Hiram Clawson
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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Re: [galaxy-user] Displaying bed files in ucsc

2012-05-11 Thread Hiram Clawson
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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Re: [galaxy-user] Displaying bed files in ucsc

2012-05-10 Thread Xianrong Wong
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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 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/



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