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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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