Cuffcompare helps you:

  • compare your assembled transcripts to a reference annotation,
  • track Cufflinks transcripts across multiple experiments (e.g. across a time course).



Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms.
C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, L. Pachter.
Nature Biotechnology (2010) 28, 511–515