Cufflinks
From ScientificComputing
Contents
Category
BioinformaticsDescription
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 |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
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 |
Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.
How to submit a job
You can submit a Cufflinks job in batch mode with the following command:sbatch [Slurm options] --wrap="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 [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system.
