Cuffcompare allows you to compare the transfrags you assemble to a reference annotation.
Cufflinks GTF from the sample is matched against the reference GTF, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. You can supply your own reference GTF or use one of the provided ones.
The analysis output consists of the following files:
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.