Software: Gffread
Description
Gffread is used to validate, filter, convert and perform various other operations on GFF files.
Available Versions
Unspecified: | 0.12.7 |
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For more information, please check its website: https://biocontainers.pro/tools/gffread and its home page: http://ccb.jhu.edu/software/stringtie/gff.shtml.
Commands
- gffread
Module
You can load the modules by:
module load biocontainers
module load gffread
Example job
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