This script takes data from nanopolish, either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py) to generate a genome browser view on a window.
pip install methplotlib
methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES [NAMES ...] -w WINDOW [-g GTF] [-b BED] [--simplify] [--split] [--smooth SMOOTH] Arguments: -h, --help show this help message and exit -v, --version Print version and exit. -m, --methylation METHYLATION [METHYLATION ...] nanoplish calls or frequency output -n, --names NAMES [NAMES ...] names of datasets in --methylation -w, --window WINDOW window (region) to which the visualisation has to be restricted -g, --gtf GTF add annotation based on a gtf file -b, --bed BED add annotation based on a bed file matching to your reference genome --simplify simplify annotation track to show genes rather than transcripts --split split, rather than overlay the methylation frequency tracks --smooth SMOOTH Smoothen the datapoints of frequencies, but reduce the details (integer, default=5)
For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.
test folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.
scripts folder contains scripts for phasing modification calls in haplotypes based on WhatsHap phasing, allele specific modification testing for phased data and differential modification testing across subjects.
TO DO - CONTRIBUTIONS WELCOME
- Outlier detection (in windows) across samples