CummeRbund - biological replicates problem

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CummeRbund - biological replicates problem

Dottorini, Tania
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
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Re: CummeRbund - biological replicates problem

Jen Hillman-Jackson
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

On 2/17/14 2:56 AM, Dottorini, Tania wrote:

> 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
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: CummeRbund - biological replicates problem

Jen Hillman-Jackson
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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

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