Scripts and pipelines for methylation calling with ONT
The snakemake pipeline calculates the weighted methylation score from Modkit (Dorado, Guppy) and DeepSignalPlant outputs and plots them over a genome. Additional stats are calculated in notebooks with papermill.
The spaces in the Modkit BED output must be replaced with tabs before passing them to Snakemake. e.g. tr ' ' '\t' < modkit.BED
The pipeline can be run with: snakemake --use-conda --cores N
Parameter should be set in the workflow/config.yaml file.
Samples should be set in the samples.csv file and then be placed into snakemake/workflow/data/
There are automated pipelines written in bash for Bismark, DeepSignalPlant, and Dorado. Dependencies must be installed manually to run these.
Files were added to show how figures or data was generated for the report.
The report can be read here