<<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?