<<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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