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
Is anyone else having this problem? And found a solution?