Hi,

I think you need to include a track line and specify "bedgraph", like this

  track type=bedGraph

Is that maybe the problem?  It sounds like UCSC is treating your file
as a standard "bed", which it will do without the track line.

Jim


On Tue, Aug 9, 2011 at 11:32 PM, John Wu <joh...@ibms.sinica.edu.tw> wrote:
>
> 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
> >
> >
> >
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of Galaxy
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>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/Support
>
>
>
>
> ___________________________________________________________
> 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
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>
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>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/

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