Plot methylation data obtained from nanopolish
Project description
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
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