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.
Versions
1.6.3
Commands
liftoff
python
python3
Module
You can load the modules by:
module load biocontainers
module load liftoff
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 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