Hi Jen,

Thanks for your answer.

However, when I followed your instructions, I found that the forth column in my 
dataset, which is the expression level (or base depth covered by short read 
sequences), would be treated as names instead of values. Therefore I cannot see 
histogram on UCSC genome browser..

Could you help me more about the question? Thanks a lot!

Please see the following link to view my dataset.

http://main.g2.bx.psu.edu/u/johnwu/h/human-bodymap2


John Wu

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, August 05, 2011 10:16 PM
To: 吳正華
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] BedGraph format

Hello John,

A file in bedgraph format should display at UCSC. I think that #3
(below) is your concern, but there are a few things to check if the display at 
UCSC link is not showing up for the dataset:

1. File is tab delimited (not space or other) and four columns, such as (from 
the UCSC web site's example: 
http://genome.ucsc.edu/goldenPath/help/bedgraph.html):

chr19   59302000        59302300        -1.0
chr19   59302300        59302600        -0.75
chr19   59302600        59302900        -0.50
chr19   59302900        59303200        -0.25
chr19   59303200        59303500        0.0
chr19   59303500        59303800        0.25

2. Use "Edit Attributes" to assign a database (click on pencil icon in 
dataset). Confirm that this database is at UCSC by matching the database short 
name "dbkey" with that used in Galaxy. If the database is not at UCSC, then 
Visualization within Galaxy is still an option (Trackster). 
You can pull in other tracks from UCSC or other sources to view all of the data 
together for custom genomes.

3. Use "Edit Attributes" to also assign the file format as "bedgraph". 
The metadata will be automatically detected. The fourth column is not 
explicitly labeled as being a data value for display, but that does not impact 
display. Not all values for all datatypes are labeled the same as external 
sites do, yet many display correctly based on the file format type assigned.

4. Optional: create a track line using "Graph/Display Data -> Build custom 
track for UCSC genome browser". This is not necessary, but does allow for some 
user-defined labels. For full control over the track and (again, optional) 
browser lines used by UCSC, create this information in a text file on your 
computer, save, load into Galaxy, and merge with the bedgraph data using "Text 
Manipulation -> Concatenate datasets tail-to-head".

If this does not help and you are still having issues on the public Galaxy 
server at http://usegalaxy.org, please send a shared history link and I can 
take a look and provide feedback ("Options -> Share or Publish, generate link, 
and email back directly to me). But, hopefully the above helps to resolve 
anything that was unclear. I just tested a bedgraph a few minutes ago, to 
confirm that there were no issue between Galaxy & UCSC for a sample bedgraph 
dataset, and it worked fine.

Best!

Jen
Galaxy team

On 8/4/11 9:01 PM, 吳正華 wrote:
> Dear all:
>
> I want to transform a text file to BedGraph format and show it on UCSC 
> genome browser, but it seems that in galaxy I cannot assign a column 
> that has values in configuration screen (BedGraph format).
>
> How should I do the above task in galaxy?
>
> Thanks
>
> John Wu
>
>
>
> ___________________________________________________________
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support




___________________________________________________________
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