It seems that the new version of the cuffdiff tool on the main galaxy mirror outputs an sqlite database ready to input into cummeRbund. However, you don't have the cummeRbund tool implemented?
What is the fastest way to get my output files extracted? I tried using RSQlite in R on my desktop but seem to be having some issues...
That's great thanks! looking forward to it.
done, see the edit on my answer