Cuffdiff finds significant changes in transcript expression, splicing, and promoter use.
Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
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