Cufflinks

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

Versions

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

Version	Owens	Cardinal
2.2.1	X*	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.

Access

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

Usage on Owens

Set-up

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