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Cufflinks

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. The package includes tools such as cufflinks, cuffmerge, cuffdiff and cuffcompare.

License

Free to use and open source under the Boost Software License 1.0.

Available

  • Roihu: 2.2.1, via the bio-apps module.

Usage

Cufflinks is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Cufflinks module:

module load bio-apps/v202603
module load cufflinks/2.2.1

To assemble transcripts from an aligned, sorted BAM file:

cufflinks -p 4 -o cufflinks_out aligned.sorted.bam

Example batch script

#!/bin/bash
#SBATCH --job-name=cufflinks
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load cufflinks/2.2.1

cufflinks -p $SLURM_CPUS_PER_TASK -o cufflinks_out aligned.sorted.bam

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information