gffread
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'gffread' Versions
- 0.12.7
Link to section 'Commands' of 'gffread' Commands
- gffread
Link to section 'Module' of 'gffread' Module
You can load the modules by:
module load biocontainers
module load gffread
Link to section 'Example job' of '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