> I got the normalized values (FPKM) from cufflinks. And I want to get relative 
> reads counts. How can I do that?

It's not clear to me what you're looking for. FPKM is a normalized read count 
metric where the F stands for fragment, which is a single read (or half of a 
paired read).

> Another question: how does cufflinks handle isoform genes while calculating 
> the reads counts?  Or what papers can help me understand this?

Expectation maximization is used to probabilistically assign reads to isoforms. 
See the Cufflinks documentation for details and paper links:

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