Please send queries such as these to the galaxy-user mailing list (cc'd); there 
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> I was wondering if you can point me to a documentation or URL to guide how to 
> perform the downstream analysis once we have cuffdiff out put.

In general, I agree that tools are needed to further process 
cufflinks/compare/diff outputs, but I'm not aware of any that are publicly 
available. Let's open this issue up for discussion and see if we can reach a 
consensus about tools might be useful. Everyone, please feel free to contribute 
ideas/tools; note that the Galaxy Tool Shed is a nice place for sharing tools 
you've built for Galaxy:


> Just like any mRNA-seq experiment to achieve following objectives:
> 1.       Reconstruct  all transcripts of a particular gene and corresponding 
> Cuffdiff  significantly expressed transcripts as called by cuffdiff.
> 2.       What are different isoforms
> 3.       Location of splicing
> From various output files which unique ID can be matched  from one file say 
> Cuffdiff.expr (transcript/ isoform/Splicing)  to  other file - transcript.gtf 
>  corresponding to each sample or combined GTF file.
I've got a script that does this for the cuffdiff isoform expression testing 
file and a GTF file; I'll wrap it up and add it to Galaxy in the next couple 
weeks. It would probably be useful to have similar scripts for the other 
expression testing files as well. Also, it would be nice to be able to take the 
FPKM values generated by Cuffdiff and attach them to their respective 
transcripts as attributes.


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