I got the normalized values (FPKM) from cufflinks. And I want to get
relative reads counts. How can I do that?
Another question: how does cufflinks handle isoform genes while
calculating the reads counts? Or what papers can help me understand
Thank you very much!
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).
Expectation maximization is used to probabilistically assign reads to
isoforms. See the Cufflinks documentation for details and paper links: