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.
Official web site: http://cole-trapnell-lab.github.io/cufflinks/assets/downloads
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 (http://cole-trapnell-lab.github.io/cufflinks/assets/downloads) CINECA consultants can be reached through the address: firstname.lastname@example.org