How To Analyze And Interpret Cuffilinks Results Without Using Igv ?

Question

[M K]

I used Cufflinks and I got the following files in the output folder. genes.fpkm_tracking isoforms.fpkm_tracking skipped.gtf transcripts.gtf

So what is the best way to interpret the results other than the visualize method.

Answer 1

[eddie.im]

Hi, You can plot some graphs with a R package. There is one called CumRbond which is very easy to use. For more details you can see on a paper called: "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks." of Nature Protocols