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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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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
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