Software: StringTie
Description
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).
Available Versions
| Unspecified: | 2.1.7 2.2.1 |
|---|
Detailed usage can be found here: https://github.com/gpertea/stringtie
Commands
- stringtie
Module
You can load the modules by:
module load biocontainers
module load stringtie
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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