Question: Extract-Cuffdiff & Plot-Cuffdiff tools missing in NGS:RNAseq
gravatar for rossi
3.5 years ago by
rossi0 wrote:


I was testing the new Cuffdiff implementation in Galaxy and I produced a Cuffdiff output in the form of "cummeRbund SQLite db". To proceed in the analysis, at least according to your NGS101 video tutorial (#16) I should find the Extract-Cuffdiff and Plot-Cuffdiff tools under the NGS:RNA analysis group but there are no such tools in the menu (I'm using Galaxy Main).

Are these tools going to be added soon? Is it possible to produce (as it was before) the individual output files to be analyzed in R with CummeRbund?



rna-seq galaxy cufflinks • 1.2k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by rossi0

Addendum: looking more closely I don't even find any "NGS:RNA analysis" group in the tools menu, as shown in the video ( In the GalaxyMain instance I'm using right now I see a "NGS:RNAseq" group.

Watching again the video I realized that the instance used there is the "", thus my question becomes: when the Galaxy Main will be updated? (I guess the update is the May2015 release (v15.05)). 

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by rossi0
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