Empty Cuffdiif Output except Gene Differential expression testing

Question

[benjyrolls]

Hello

I am running a Cuffdiff on two separate conditions of a file.

all outputs seem to be empty except the gene differential expression output which shows the deferentially expressed genes.

does it mean this output is wrong.

i have followed other similar outputs on the forum but cant get this to work.

Also what is the best way to run Cuffdiff after mapping with Tophat, is it always necessary to run Cufflinks, followed by cuffcompare before Cuffdiff or we could run cufffdiff on the mapped bam files using a GTF file from UCSC browser?

Benjy