megadepth
Link to section 'Introduction' of 'megadepth' Introduction
Megadepth
is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files.
For more information, please check its website: https://biocontainers.pro/tools/megadepth and its home page on Github.
Link to section 'Versions' of 'megadepth' Versions
- 1.2.0
Link to section 'Commands' of 'megadepth' Commands
- megadepth
Link to section 'Module' of 'megadepth' Module
You can load the modules by:
module load biocontainers
module load megadepth
Link to section 'Example job' of 'megadepth' 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 Megadepth on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=megadepth
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers megadepth
megadepth sorted.bam