Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.

Availability and Restrictions


Cufflinks is available on the Owens Cluster. The versions currently available at OSC are:

Version Owens
2.2.1 X*
* Current Default Version

You can use module spider cufflinks to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


Cufflinks is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Cole Trapnell et al., Open source


Usage on Owens


To configure your enviorment for use of Cufflinks, use command module load cufflinks. This will load the default version.

Further Reading

Fields of Science: