StringTie

Introduction

StringTie: efficient transcript assembly and quantitation of RNA-Seq data.

Stringtie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome. It takes as input spliced alignments in coordinate-sorted SAM/BAM/CRAM format and produces a GTF output which consists of assembled transcript structures and their estimated expression levels (FPKM/TPM and base coverage values).

Detailed usage can be found here: https://github.com/gpertea/stringtie

Versions

• 2.1.7

• 2.2.1

Commands

• stringtie

Module

You can load the modules by:

module load biocontainers
module load stringtie

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run stringtie on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=stringtie
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers stringtie

stringtie -o SRR11614710.gtf -G Homo_sapiens.GRCh38.105.gtf SRR11614710Aligned.sortedByCoord.out.bam