Hello David,

This is a known bug. The correction is planned to be moved out onto the public Galaxy instance at the next update (within a week).


Sorry for the current inconvenience,

Best,

Jen
Galaxy team

On 8/19/11 7:00 AM, David K Crossman wrote:
Hello!

I have an RNA-Seq project which consists of 5 samples from the species
tree shrew. When uploading these fastq files into Galaxy, I chose
“unspecified (?)” for the database/build since the latest tree shrew
version is not in the drop down list. When using TopHat,
Cufflinks/Compare I have selected a reference genome from my history
instead of using a built-in index, as well as a gtf annotation file for
Cufflinks/Compare and everything has been working fine. Now, I am at the
Cuffdiff step and I am running into an error when setting it up to
perform replicate analysis. When I select my TopHat accepted hits bam
file I see a red X and the error: “Unspecified genome build, click the
pencil icon in the history item to set the genome build.” Here’s a
screenshot of what I’m seeing:

Since the latest reference genome for tree shrew wasn’t listed, that’s
why I chose “unspecified (?).” Should I go back and edit these accepted
hits bam files to say the Database/Build from the drop down list is
“Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?” I know that this is
simple to change, but will this affect my results in any way? Any
help/info would be greatly appreciated.

Thanks,

David



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