Hello everyone,

I am comparing two samples (control and treated) paired end RNA Seq data.
In the cuffdiff output I have noticed that few genes have zero FPKM value
in one sample and other sample has significant FPKM value.
I want to identify uniquely expressed genes identified only in one sample
(either control or treated).

My question: If something is measured with significance in one sample (high
FPKM), but not measured at all in another sample (Zero FPKM), should I
consider that gene as significant?

Can anyone explain this.


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