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