Question: Cuffdiff Question About Using An Unspecified (?) Database/Build
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David K Crossman • 130 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:
[cid:image001.png@01CC5E4E.76F37AF0]
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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modified 7.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
7.3 years ago by
David K Crossman • 130
