I am confused about the first line in cuffdiff (using Galaxy on the cloud, not sure if it's different for local instances). It reads:

Transcripts:(choose a file)A transcript GTF file produced by cufflinks, cuffcompare, or other source.

What file should I load here? I have 4 groups of 2-4 replicates each that I am comparing, and am using the "grouping" option that follows. Should I use one of the files produced by cufflinks? If so, which ones? Or should I rather use the GTF file of RefSeq genes from the UCSC database?
Thx!!A