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 group2.0
 
<<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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