Bismark

Introduction

Bismark is a tool to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step

For more information, please check:
BioContainers: https://biocontainers.pro/tools/bismark
Home page: https://github.com/FelixKrueger/Bismark

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

0.23.0, 0.24.0

BELL

0.23.0, 0.24.0

GAUTSCHI

0.23.0, 0.24.0

NEGISHI

0.23.0, 0.24.0

SCHOLAR

0.23.0, 0.24.0

Commands

  • bismark

  • bam2nuc

  • bismark2bedGraph

  • bismark2report

  • bismark2summary

  • bismark_genome_preparation

  • bismark_methylation_extractor

  • copy_bismark_files_for_release.pl

  • coverage2cytosine

  • deduplicate_bismark

  • filter_non_conversion

  • methylation_consistency

  • –

  • Bismark

  • has

  • Samtools

  • Bowtie2

  • and

  • HISAT2

  • inside.

  • Should

  • we

  • –

  • alias

  • them

  • for

  • the

  • user

  • as

  • well

  • or

  • keep

  • them

  • internal?

  • –

  • Keep

  • hidden

  • for

  • now.

Module

You can load the modules by:

module load biocontainers
module load bismark

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 bismark on our clusters:

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

module --force purge
module biocontainers bismark

# Your bismark workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bismark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bismark

# Your bismark workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bismark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bismark

# Your bismark workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bismark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers bismark

# Your bismark workflow...

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

module --force purge
module biocontainers bismark

# Your bismark workflow...