deepsignal2
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'deepsignal2' Versions
- 0.1.2
Link to section 'Commands' of 'deepsignal2' 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
Link to section 'Module' of 'deepsignal2' Module
You can load the modules by:
module load biocontainers
module load deepsignal2
Link to section 'Example job' of 'deepsignal2' 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 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