bam-readcount
Link to section 'Introduction' of 'bam-readcount' Introduction
Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.
Docker hub: https://hub.docker.com/r/mgibio/bam-readcount and its home page on Github.
Link to section 'Versions' of 'bam-readcount' Versions
- 1.0.0
Link to section 'Commands' of 'bam-readcount' Commands
- bam-readcount
Link to section 'Module' of 'bam-readcount' Module
You can load the modules by:
module load biocontainers
module load bam-readcount
Link to section 'Example job' of 'bam-readcount' 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 Bam-readcount on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bam-readcount
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bam-readcount
bam-readcount -f Homo_sapiens.GRCh38.dna.primary_assembly.fa Aligned.sortedByCoord.out.bam