RNA-Seq - From Cufflinks FPKM to differential gene expression

[aituka]

Hello,

I recently started working with RNA-Seq. I have a study with 8 samples divided in 2 groups (let say A and B). I applied the tophat-cufflinks pipeline. As a result, for each file, i have "genes.fpkm_tracking" which contains the fpkm for each read.

The question is : is it possible to estimate the differential gene expression between these 2 groups based only on these fpkm results.

(i read a post from Simon Anders where i think he was suggesting that this is impossible. but this post was old and anyway i can't find it again).

If not, what is the point of using Cufflinks?

thanks

[IBseq]

Hi Aituka,
CUFFLINKS output is used as INPUT for cuffdiff, which anlayses the fpkm values betwseen the samples to give you differential expression. alternatively u can use a refence annotation rather than cufflinks, but cuffdiff requires certain attributes which the reference annotation does not have

hope it helps.
ib