identify different number of differential expressed genes using ensemble or reseq GTF

[sepulveda]

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.