Transcript assembly, differential expression and regulation for RNA-Seq

 Cufflinks assembles transcripts, estimates their abundances, and tests for
 differential expression and regulation in RNA-Seq samples. It accepts aligned
 RNA-Seq reads and assembles the alignments into a parsimonious set of
 transcripts. Cufflinks then estimates the relative abundances of these
 transcripts based on how many reads support each one.