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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.

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions
2.1.1, 2.2.1

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
2.1.1 module load gcc/4.8.2 boost/1.57.0 eigen/3.2.1 cufflinks/2.1 openblas/0.2.13_seq python/2.7.6
2.2.1 module load legacy gcc/4.8.2 python/2.7.6 samtools/1.1 boost/1.55.0 eigen/3.2.1 openblas/0.2.13_seq

How to submit a job

You can submit a Cufflinks job in batch mode with the following command:
bsub [LSF options] "Cufflinks [cufflinks options]"
Here you need to replace [cufflinks options] with Cufflinks command line options (please run cufflinks -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

License information

BOOST software license