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.goecks@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

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