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 [[email protected]]
Sent: Thursday, February 09, 2012 4:00 AM
To: Li, Jilong (MU-Student)
Cc: [email protected]
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
[email protected]
www.lcosme.com
-----------------------------------
___________________________________________________________
The Galaxy User list should be used for the discussion of
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