Read group info isn't included in the Cuffdiff output right now. I've created a 
Trello card to fix this oversight: https://trello.com/c/FdUYdbIn

Best,
J.

On Feb 18, 2013, at 12:32 PM, Johanna Sandgren wrote:

> Hi,
>  
> I am running cufflinks and cuffdiff using Galaxy. I am however wondering if 
> it is not supposed to be output files from cuffdiff regarding each replicate. 
> Anyone know why those (read.group-files) are not there, or when they will be 
> if it is because of the version used in Galaxy. I find it very valuable to 
> have those to be able to see intra/inter-group features in downstream 
> analysis.
>  
> Thanks,
> Johanna
>  
> ......................................................................................................................................................
> Johanna Sandgren, PhD
> Department of Oncology-Pathology
> CCK, Karolinska Institutet
> SE-171 76 Stockholm, Sweden
> +46-8-517 721 35 (office),
> +46-8- 321047(fax), +46-708 388476 (mobile)
>  
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