methplotlib 0.14.1

Plot methylation data obtained from nanopolish

METHPLOTLIB

This script generates a browser view on a window using data from
i) nanopolish, either as methylation calls or methylation frequencies (as processed by calculate_methylation_frequency.py)
ii) nanocompore
iii) in ont-cram format with MM/MP tags according to the SAM specifications and converted using e.g. this script

INSTALLATION

pip install methplotlib

USAGE

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.
  -example             Show example command and exit.

  -m, --methylation METHYLATION [METHYLATION ...]
                        methylation data in nanopolish, nanocompore or ont-cram format
  -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
  -f, --fasta FASTA     required when --window is an entire chromosome, contig or transcript

  --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)
  --dotsize DOTSIZE     Control the size of dots in the per read plots
  -o, --outfile OUTFILE File to write results to. Default: methylation_browser_{chr}_{start}_{end}.html.
                        Use {region} as a shorthand for {chr}_{start}_{end} in the filename.
                        Missing paths will be created.
  -q, --qcfile QCFILE   File to write the qc report to. Default: The path in outfile prefixed with qc_,
                        default is qc_report_methylation_browser_{chr}_{start}_{end}.html.
                        Use {region} as a shorthand for {chr}_{start}_{end} in the filename.
                        Missing paths will be created.

Snakemake workflow

For streamlining nanopolish a Snakefile is included (using snakemake). The workflow uses a config file, of which an example is in this repository.

Example data

The examples folder contains calls and frequencies for the human ACTB gene from PromethION sequencing of NA19240. An example command is available.

Companion scripts

The 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