Each sample is matched against the reference, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. You can supply your own GTF or use one of the provided ones.
Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you:
The analysis output consists of the following:
This tool uses the Cufflinks package for statistical analysis. Please read the following article for more detailed information:
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.