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.

Version: 2.2.1

Availability: GALILEO100

Target: academic

Official web site:

Related Commands:

Setup the environment with the command:

module load cufflinks

Help and Documentation:

You can find documentation on the system, with the command:

module help cufflinks 

The manual is on the web at the original home page ( CINECA consultants can be reached through the address: