Cummerbund - Biological Replicates Problem

Question: Cummerbund - Biological Replicates Problem

4.8 years ago by

European Union

Dear all, I would like to visualise by CummeRbund the Cuffdiff results obtained using the cufflinks/cuffdiff workflow on the Galaxy server. My samples include replicates data and when I ask for analysis to be done by CummeRbund, to compare replicates, I get error messages. From past postings I red that the Galaxy Cuffdiff does not allows you to download all the required files to be used by CummeRbund for replicate comparisons. As far as I know, the only way to overcome this problem is to run local computer Cuffdiff. I would like to know if anything has changed so far concerning Galaxy Cuffdiff output files and if there are other options instead of running local computer Cuffdiff to solve this problem. Any help would be appreciated Thank you Tania

rna-seq cufflinks • 1.5k views

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modified 4.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.8 years ago by Dottorini, Tania • 20

4.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Tania, Read group info was recently introduced as of the updates to the public Main server and source distribution on 2/10/2014 (last Monday). The ticket for the change is here: https://trello.com/c/FdUYdbIn As far as I know, this was the missing piece that permitted result use in CummeRbund. This is other work requested or in progress for this tool suite, and you can track progress (and up-vote) development tickets here: https://trello.com/c/lIdpOZ88 https://trello.com/c/U7nceKdj https://trello.com/c/GKx77bnL https://trello.com/c/CL4YOsdR If there is more to share about these tools, we will post an updated reply. Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.8 years ago by Jennifer Hillman Jackson ♦ 25k

4.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

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