[galaxy-user] How to get reads counts from cufflins?

Hi all, 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 this? Thank you very much!

Re: [galaxy-user] How to get reads counts from cufflins?

Victor, 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).

Re: [galaxy-user] How to get reads counts from cufflins?

From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Thursday, February 09, 2012 4:00 AM To: Li, Jilong (MU-Student) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to get reads counts from cufflins? Victor, I got the normalized values (FPKM) from

Re: [galaxy-user] How to get reads counts from cufflins?

. Could you please tell me how to get those? Thank you very much! Victor From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Thursday, February 09, 2012 4:00 AM To: Li, Jilong (MU-Student) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] How to get reads