Cuffdiff Visualization

[jdanderson]

Hello All,

How are some of you visualizing the Cuffdiff output files?

Is it just a matter of parsing (via a script) the FPKM and p-values out of the file and visualizing them in something akin to R?

Is anyone ranking there outputs according to p-values or is everyone just going with the log of FPKM values?

Any guidance or suggestions would be most appreciated.

Cheers,
Johnathon

[jdanderson]

Hello All,

Just wondering if anyone could provide some type of feedback on how they are visualizing the Cuffdiff gene and isoform FPKM values? I've written a script to parse and sort the log of FPKMy/FPKMx along with its chromosomal location, filtering out the ones that aren't called significant. I ended up with over 900 genes still and I was wondering how people have been dealing with this kind of data outside of heatmaps, and how they were dealing with representing differential isoform expression?

Any thoughts on the matter would be most appreciated.

Regards,
Johnathon

[honey]

Has anyone figured out how we can visulaize the output of Cuffdiff for RNA seq analysis?