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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.

StringTie

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It can be used for transcript assembly and quantification, either de novo or guided by a reference annotation.

License

Free to use and open source under the MIT License.

Available

  • Roihu: 3.0.3, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load stringtie/3.0.3

Assemble transcripts from a sorted BAM file, optionally guided by a reference annotation:

stringtie aligned.sorted.bam -G annotation.gtf -o assembled.gtf -p 8

Example batch script

#!/bin/bash
#SBATCH --job-name=stringtie
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load stringtie/3.0.3

stringtie aligned.sorted.bam -G annotation.gtf -o assembled.gtf -p $SLURM_CPUS_PER_TASK

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