crossmap
Link to section 'Introduction' of 'crossmap' Introduction
Crossmap is a program for genome coordinates conversion between different assemblies.
For more information, please check its website: https://biocontainers.pro/tools/crossmap and its home page: https://crossmap.readthedocs.io/en/latest/#convert-maf-format-files.
Link to section 'Versions' of 'crossmap' Versions
- 0.6.3
Link to section 'Commands' of 'crossmap' Commands
- CrossMap.py
Link to section 'Module' of 'crossmap' Module
You can load the modules by:
module load biocontainers
module load crossmap
Link to section 'Example job' of 'crossmap' 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 Crossmap on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=crossmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers crossmap
CrossMap.py bed GRCh37_to_GRCh38.chain.gz test.bed