Replicate analysis via Cuffdiff can yield different results as compared to 
single sample analysis via Cufflinks. See this FAQ for details:

http://cufflinks.cbcb.umd.edu/howitworks.html#reps

Best,
J.

On May 31, 2012, at 10:55 AM, Jia Meng wrote:

>  
> <<Problem>>
> The cufflinks and cuffdiff results are not consistent with each other. This 
> is killing me.
> Does it make sense?
>  
> << Obseration >>  
> We have 3 control samples and 3 treated sample. For many genes, their FPKM in 
> cufflinks and cuffdiff are far from consistent. In cufflinks result, for a 
> gene’s FPKM are
> control group (sample: 1,2,3):0, 0, 4.8
> treated group(sample: 1,2,3):0, 0, 6.0
>  
> In cuffdiff, the estimated FPKM are
> control group: 12.6
> treated group:2.0
>  
> <<Method>>
> Use ucsc gene annotation gtf file, mm9, downloaded from UCSC table database
>  
> Use cufflinks on each individual sample.
> Cufflinks: galaxy mirror at cistrome, minimal count:10, no quantile 
> normalization, use gtf as reference, no background correction
>  
> Use cufflinks on treated groups (3 biological replicates) and control groups 
> (3 biological replicates)
> Cuffdiff: galaxy mirror at cistrome, minimal count:10, no normalization, use 
> gtf as reference, no background correction
>  
> <<Additional Comments>>
> Cufflinks returns 55350 transcripts, while cuffdiff return 55418 transcripts, 
> even though they use the same gene annotation gtf file.
> For the 6 cufflinks results (corresponding to 6 samples), the transcript ids 
> are all the same, but the order are not,
>  
> <<Question>>
> Does it make sense? Or did I do anything wrong?
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