methplotlib 0.2.0

Plot methylation data obtained from nanopolish

METHPLOTLIB

This script takes data from nanopolish as processed by calculate_methylation_frequency.py to generate a genome browser view on a window.

INSTALLATION

pip install methplotlib

USAGE

methplotlib [-h] -m METHYLATION [METHYLATION ...] -n NAMES [NAMES ...]
                   -w WINDOW [-g GTF] [--simplify] [--split] [--smooth SMOOTH]

plotting methylation frequency

optional arguments:
  -h, --help            show this help message and exit
  -m, --methylation METHYLATION [METHYLATION ...]
                        output file(s) from calculate_methylation_frequency.py
  -n, --names NAMES [NAMES ...]
                        names of datasets in --methylation
  -w, --window WINDOW   window (region) to which the visualisation has to be
                        restricted e.g. chr7:12345-23456
  -g, --gtf GTF         add annotation based on a gtf file matching to your
                        reference genome
  --simplify            simplify annotation track to show genes rather than transcripts
  --split               split, rather than overlay the methylation tracks
  --smooth SMOOTH       Smoothen the datapoints, but reduce the details (integer, default=5)

TO DO - CONTRIBUTIONS WELCOME

• Adapt to also use methylation data from tombo
• Add plot showing (pairwise) correlation between methylation results
• Add a mode to plot raw methylation signals rather than summarized frequencies
• Differential methylation analysis (in windows) across groups of samples
• Outlier detection (in windows) across samples
• Add pipeline and visualization for phased methylation
• Think about adding a coverage track - maybe based on the called_sites column