Hi Victor,
I also wanted to get the count reads but it did not work with Cufflinks. You can use GenomicRanges package (Bioconductor). I am also using Deseq (negative binomial distribution) to detect the differentially expressed genes from time series data. You can find it here http://bioconductor.org/packages/release/bioc/html/DESeq.html
Best,

Luciano

On Feb 8, 2012, at 10:18 PM, Jeremy Goecks wrote:

Reads are probabilistically assigned, so raw read counts are not available from Cufflinks.

Recovering raw fragment counts could be done by reverse-engineering the FPKM value, but Cufflinks doesn't do this for you. If you choose to do this, keep in mind that Cufflinks uses an "effective transcript length".

Best,
J.

On Feb 8, 2012, at 11:06 PM, Li, Jilong (MU-Student) wrote:

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!

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 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).

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:

http://cufflinks.cbcb.umd.edu/

Best,
J.

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-----------------------------------
Luciano Cosme
PhD Candidate
Texas A&M Entomology
co...@tamu.edu
www.lcosme.com
-----------------------------------





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