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:j...@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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support

___________________________________________________________
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