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.

• StringTie
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• StringTie home page

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