cufflinks: cufflinks (A reference-guided assembler for RNA-Seq experiments) cufflinks: cufflinks: Cufflinks assembles transcripts, estimates their abundances, cufflinks: and tests for differential expression and regulation in RNA- cufflinks: Seq samples. It accepts aligned RNA-Seq reads and assembles cufflinks: the alignments into a parsimonious set of transcripts. cufflinks: cufflinks: Home: http://cufflinks.cbcb.umd.edu/ cufflinks: References: /usr/doc/cufflinks-2.2.1/References cufflinks: cufflinks: