Hello Victor,

This is OK for use with single-end reads. But, if you have questions about how to exactly interpret the values, the Cufflinks authors would be a good resource, the contact information is in the example of this wiki Support section:
http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result

Hopefully this helps,

Best,

Jen
Galaxy team

On 11/3/11 12:44 PM, Li, Jilong (MU-Student) wrote:
Hi,

I want to use cufflinks handle the results of Tophat. Cufflinks uses
FPKM to normalize the expression data. I think FPKM is for pair-end
reads. right? My reads are single-end. Is it right if I use FPKM?

Thank you very much!

Victor


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