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
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at usegalaxy.org. Please keep all replies on the list by
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