Hi Tania, Yes, you are correct, the count files only address a portion of the new features. Recent updates to the underlying tools in the Tuxedo suite have resulted in issues of this sort as well (among others). The current plan is to continue with development to enhance the tool wrappers in Galaxy to support as much downstream analysis as practical. I created a new ticket as a catch-all to address this need in a global way. Details will be added as work progresses. https://trello.com/c/ugu8dty0 This is a timely and important inquiry. Our user & development community feedback is an important component in how work is prioritized. _/I encourage you and others interested in this enchantment to "up-vote" the ticket/__/in Trello./_ Comments are also welcome. Trello help: https://wiki.galaxyproject.org/Issues Best, Jen Galaxy team On 2/18/14 5:45 AM, Dottorini, Tania wrote:

Hi Jennifer,

Thanks for your help, I did my Cuffdiff runs on 2/12/2014 but still I was not able to analyse replicates by CummerBund. The output of replicates(cuff) is empty.

Thank you Tania

-- Jennifer Hillman-Jackson http://galaxyproject.org