Gffread

Introduction

Gffread is used to validate, filter, convert and perform various other operations on GFF files.

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

Versions

• 0.12.7

Commands

• gffread

Module

You can load the modules by:

module load biocontainers
module load gffread

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 Gffread on our clusters:

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

module --force purge
ml biocontainers gffread

gffread -E annotation.gff -o ann_simple.gff

gffread annotation.gff -T -o annotation.gtf

gffread -w transcripts.fa -g genome.fa annotation.gff