I am analyzing significant differential expressed genes for a pair of
normal V.S tumor, using Cuffdiff 2.0.2.
I noticed that by using ensemble GTF and refseq GTF, the results showed a
big difference on the number of genes being significant expressed.
For ensemble GTF, there are only 250 genes differential expressed.
But for refseq GTF, there are about 1000 genes.
I am running these data on Galaxy server and with the same workflow.
Can anyone explain what is going on here? so which result should I trust?
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
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