Thanks for the information. I've added an option to the Cuffdiff tool so that the read group files can be output by Galaxy; this should make it possible to run Cuffdiff in Galaxy and then Cummerbund for replicate analysis. This change will make it out to our public server in a couple weeks.
Thanks, J. On Jul 31, 2013, at 5:39 PM, Mike Shamblott wrote: > Thanks > > My tests confirm that cummerbund does require the run group files to do > replicate analyses. Therefore Galaxy cannot be used to do cuffdiff on > replicates when cummerbund is the next step in the workflow. > > Mike > > > > Sent from my iPhone > > On Jul 31, 2013, at 9:45 AM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote: > >> In the past, others have had success using Cummerbund with Galaxy, and >> there's even a Cummerbund wrapper in the tool shed: >> >> http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund >> >> That said, it appears that replicate information is largely contained in the >> read group tracking files, which are not currently included in Galaxy's >> Cuffdiff outputs. I don't know if these files are required by Cummerbund to >> do replicate analysis. This would be a good question for the Cummerbund >> developers, as well as what the p and q values mean when doing replicate >> analysis. >> >> If you find that Galaxy's lacking something for Cummerbund to function >> correctly, that would be very useful information to share with the list. >> >> Best, >> J. >> >> >> On Jul 26, 2013, at 8:50 PM, Mike Shamblott wrote: >> >>> I'm trying to run Cuffdiff on a set of 10 human samples with biological >>> replication then download the results for further analyses in >>> Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get >>> cummerbund to acknowledge replicates. I download and rename the 11 >>> cuffdiff output files to the names expected by cummerbund. Cummerbund >>> builds a CuffSet with no warnings and most analyses work as expected. The >>> problem comes any time I try to see the results of replication. For >>> example, in cummerbund, >replicates() returns an empty set and any type of >>> plot returns an error when replicates=T is included as an argument. >>> >>> There is no evidence of replication data in any of the 11 cuffdiff output >>> files. The data is presented with the group name only. From this, I >>> conclude that the problem is with cuffdiff, since there is no replicate >>> data for cummerbund to build into its db. I see that there are several >>> read group files that are produced by cuffdiff but cannot be downloaded in >>> Galaxy. Is this the problem, and if so, how can Galaxy be used to generate >>> data with (essential) replication? Are the p and q significance values >>> reported in the output files a result of replicate analysis? >>> >>> I have tried to ask this question in several different forums without >>> success. The responses I've gotten suggest its a Galaxy issue rather than >>> either cuffdiff or cummerbund. I'm hoping someone here can help answer my >>> questions. >>> >>> Hopeful, >>> >>> Mike >>> >>> >>> ___________________________________________________________ >>> 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/ >>
___________________________________________________________ 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/