Cufflinks v2.1.1

Bluebear >> Applications and Printing

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.

This page has the following sections:

Changes since previous version

This is the first release of this application on the BlueBEAR service


Support Level 

The Support Level for this application is An


Accessing the Software

Prior to the first use of this application use the command

module load apps/cufflinks

To access this particular version of the software, rather than the default version which will change as new versions are released, use the command

module load apps/cufflinks/v2.1.1

For continuity as new versions are released, the version-specific module command will be used throughout this help page.


Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service


Known Problems and Limitations



Associated Software



Other Information Sources

First-line support is available from the IT Service Desk .

See the Cufflinks website for more information about this application


Last modified: 22 May 2014