liftoff
Link to section 'Introduction' of 'liftoff' Introduction
Liftoff is an accurate GFF3/GTF lift over pipeline.
For more information, please check its website: https://biocontainers.pro/tools/liftoff and its home page on Github.
Link to section 'Versions' of 'liftoff' Versions
- 1.6.3
Link to section 'Commands' of 'liftoff' Commands
- liftoff
- python
- python3
Link to section 'Module' of 'liftoff' Module
You can load the modules by:
module load biocontainers
module load liftoff
Link to section 'Example job' of 'liftoff' 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 Liftoff on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=liftoff
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers liftoff
liftoff -g reference.gff3 -o target.gff3 \
-chroms chr_pairs.txt target.fasta reference.fa