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, taking into account biases in library preparation protocols.

Cufflinks was originally developed as part of a collaborative effort between the Laboratory for Mathematical and Computational Biology, led by Lior Pachter at UC Berkeley, Steven Salzberg’s computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold’s lab at Caltech. The project is now maintained by Cole Trapnell’s lab at the University of Washington.






To see what other modules are needed, what commands are available and how to get additional help type

module help cufflinks

To see what versions of Cufflinks are available type

module avail cufflinks

To use Cufflinks, include a command like this in your batch script or interactive session to load the Cufflinks module:

module load cufflinks

Be sure you also load any other modules needed, as listed by the module help cufflinks command.