Gffcompare

Introduction

Gffcompare is used to compare, merge, annotate and estimate accuracy of one or more GFF files.

For more information, please check its website: https://biocontainers.pro/tools/gffcompare and its home page: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml.

Versions

0.11.2

Commands

gffcompare

Module

You can load the modules by:

module load biocontainers
module load gffcompare

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 Gffcompare on our clusters:

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

module --force purge
ml biocontainers gffcompare

gffcompare -r annotation.gff transcripts.gtf