Cuffdiff with 2 conditions and time series

Question

[KL]

Hi,

I have KO and WT with 3 replicates and 2 time points (RNA-Seq). How do I use cuffdiff with the time series option? How can I interpret the result file?

So far my pipeline has been tophat2 > samtools index > cufflinks > transcripts.gtf > cuffmerge.

I am googling for 2 days and so far I didn't find a satisfying answer. I hope somebody help me on this.

Cheers
Kerstin