RNA-Seq - From Cufflinks FPKM to differential gene expression

aituka · 03-18-2012, 05:34 AM

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 · 07-29-2012, 11:20 AM

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

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03-18-2012, 05:34 AM	#1
aituka Member Location: brussels Join Date: Mar 2012 Posts: 13	RNA-Seq - From Cufflinks FPKM to differential gene expression 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

07-29-2012, 11:20 AM	#2
IBseq Member Location: uk Join Date: Jul 2012 Posts: 56	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