Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
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-bounces@lists.bx.psu.edu [mailto:galaxy-user- bounces@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: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
___________________________________________________________ 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:
-- 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:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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-bounces@lists.bx.psu.edu [mailto:galaxy-user- bounces@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: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
___________________________________________________________ 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:
-- 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:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
participants (2)
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Jennifer Jackson -
Robert Curtis Hendrickson