Question: Re: Downstream Analysis Of Cuffdiff Out Put
7.7 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Jagat, Please send queries such as these to the galaxy-user mailing list (cc'd); there are many users on the list who can contribute to this discussion, and there are many additional users that will benefit from this discussion. 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: http://community.g2.bx.psu.edu/ 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. Best, J.
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