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-------- Original Message --------
Subject: Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
Date: Thu, 25 Aug 2011 08:41:21 -0700
From: Jennifer Jackson <j...@bx.psu.edu>
To: Robert Curtis Hendrickson <curt...@uab.edu>
CC: 'galaxy-...@lists.bx.psu.edu' <galaxy-...@lists.bx.psu.edu>, David K Crossman <dkcro...@uab.edu>

Hi Curtis,

Changeset details:
http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9

We are planning on releasing a distribution within a week, so
alternatively you could wait and pull from there, if you normally work
from the galaxy-dist repository.

And for everyone tracking this fix: the changeset was applied to the
public Galaxy main instance yesterday (http://usegalaxy.org).

Hope this helps!

Jen
Galaxy team

On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote:
Jen,

Can you also please describe the details of the fix?
We need to fix the same issue in our local instance, but don't know if this was 
a fix to cuffdiff, or to galaxy. Which one should we be updating?

Regards,
Curtis


-----Original Message-----
From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
boun...@lists.bx.psu.edu] On Behalf Of David K Crossman
Sent: Friday, August 19, 2011 11:10 AM
To: Jennifer Jackson
Cc: galaxy-user (galaxy-user@lists.bx.psu.edu)
Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?)
database/build

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



___________________________________________________________
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:

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To manage your subscriptions to this and other Galaxy lists, please
use the interface at:

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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/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/
___________________________________________________________
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/

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