Deepsignal2

Introduction

Deepsignal2 is a deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads.

For more information, please check its home page on Github.

Versions

• 0.1.2

Commands

• deepsignal2

• call_modification_frequency.py

• combine_call_mods_freq_files.py

• combine_two_strands_frequency.py

• concat_two_files.py

• evaluate_mods_call.py

• filter_samples_by_label.py

• filter_samples_by_positions.py

• gff_reader.py

• randsel_file_rows.py

• shuffle_a_big_file.py

• split_freq_file_by_5mC_motif.py

• txt_formater.py

Module

You can load the modules by:

module load biocontainers
module load deepsignal2

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 Deepsignal2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=deepsignal2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers deepsignal2