[galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

Hi all, 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? Thanks. -- Wei Liao Research Scientist, Brentwood Biomedical Research Institute 16111 Plummer St. Bldg 7, Rm D-122 North Hills, CA 91343 818-891-7711 ext 7645