Dear Jeremy,

Sorry, I didn't expressed my question clearly. I got the FPKM normalized values 
for each gene from cufflinks. And I want to get the original reads counts that 
were not normalized from cufflinks. Could you please tell me how to get those?

Thank you very much!


From: Jeremy Goecks []
Sent: Thursday, February 09, 2012 4:00 AM
To: Li, Jilong (MU-Student)
Subject: Re: [galaxy-user] How to get reads counts from cufflins?


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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