Hi Luobin,

To display at UCSC, the datatype has to be a UCSC display type and the database has to be a UCSC genome browser. Often, small changes can be made to tune a dataset to help it fit into these requirements. Other times, a dataset will need to be transformed into another type or it can't be viewed at all because the genome is not available at UCSC.


You should try to modify these attributes yourself first. Common UCSC datatypes from Galaxy are: BED, bigBED, BAM. For the list of UCSC known datatypes, see: http://genome.ucsc.edu/FAQ/FAQformat.html.

Known databases would be any that you also can find at:
http://genome.ucsc.edu as full genome assemblies. The short label used at UCSC should match the database assignment at Galaxy. For example, the most recent human would be "hg19" at both.

If you are still stuck and would like to send me a shared history link, I can provide feedback about how to modify (if possible) to view at UCSC. Use "Options -> Share or Publish", generate the link, and email this link directly back to me. Be sure to include the dataset #, so that I know which in your history you want to view at UCSC.

Best,

Jen
Galaxy team

On 2/14/12 11:50 AM, Luobin Yang wrote:
Hi,

I have a local instance of Galaxy, but I found there is no "Display at
UCSC Main" link for some datasets that can be viewed in GeneTrack or
displayed by Ensemble, what has been wrong?

Thanks,
Luobin


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