Elwood,
Would you please share:
1. an original history that worked (if possible)
2. the workflow you are using and let me know how you generated (did you
extract it recently (last week or so)?
3. problem history
There are a few known issues in here, some mitigated, one that has to do
with extracted workflows from existing older histories that is Cuffdiff
specific (actually, a few problems, found another last night). I want to
rule those out or at least try to provide feedback.
I am at a conference over next several days, so let's use galaxy-bugs as
a cc whenever we communicate so nothing is left lingering, plus I know
Nate was looking into some of your data. Jeremy may jump also in at any
time and help - he is the author of the wrapper.
So, in your *reply*, _remove galaxy-u...@bx.psu.edu_ and _add
galaxy-b...@bx.psu.edu_
Jen
Galaxy team
On 10/22/13 5:42 AM, Elwood Linney wrote:
After successfully using RNAseq software in Galaxy online for about
10 different datasets to just get gene expression differences between
replicates from control versus exposed zebrafish embryos, I am having
no luck getting cuffdiff to work with the "moved" Galaxy.
I had this problem with histories developed before the move and
histories developed after the move.
I have had this problem using an order cuffmerge gtf file that worked
in the past in Cuffdiff, with a new cuffmerge file developed from
cufflinks of the files and by just using a ref file gtf from UCSC.
I don't know if this is just some interface problem with a different
version of the software that was included with the move, or a
reference genome that does not interface with Cuffdiff. It has
happened with about 5 different histories.
Is anyone else having this problem? And found a solution?
Elwood Linney
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The Galaxy User list should be used for the discussion of
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