Jen, Thank you very much for the reply. I'm glad to know it is a known bug and not something on my side of things. So, would my analysis be affected if I did change the bam file "Database/Build" to the older tree shrew version found in the drop down list? What significance does this "Database/Build" box have in downstream analysis if you have your own fasta reference genome file and gtf annotation file that is being referenced instead of a locally cached one? I'm just trying to obtain a better understanding of the "Database/Build" box for analyses where I provide the fasta and gtf file. Thanks, David -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, August 19, 2011 9:20 AM To: David K Crossman Cc: galaxy-user (galaxy-user@lists.bx.psu.edu) Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build 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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