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
___________________________________________________________
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/
