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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