Bamliquidator

Introduction

Bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.

For more information, please check its | Docker hub: https://hub.docker.com/r/bioliquidator/bamliquidator/ and its home page on Github.

Versions

  • 1.5.2

Commands

  • bamliquidator

  • bamliquidator_bins

  • bamliquidator_regions

  • bamliquidatorbatch

Module

You can load the modules by:

module load biocontainers
module load bamliquidator

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 Bamliquidator on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bamliquidator
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers bamliquidator