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-user@bx.psu.edu and add galaxy-bugs@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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