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). The methylation calls can additionally be phased using scripts/annotate_calls_by_phase.and scripts/split_calls_by_phase.py
ii)
nanocompore
iii) in ont-cram format with MM/MP tags according to the SAM specifications and converted using e.g.
this script
iv) in bedgraph format
INSTALLATION
Creating a new conda environment:
conda create -n methplotlib methplotlib
Or using pip:
pip install methplotlib
USAGE
methplotlib [-h] [-v] -m METHYLATION [METHYLATION ...] -n NAMES
[NAMES ...] -w WINDOW [-g GTF] [-b BED] [-f FASTA]
[--simplify] [--split] [--static STATIC] [--smooth SMOOTH]
[--dotsize DOTSIZE] [--example] [-o OUTFILE] [-q QCFILE]
plotting nanopolish methylation calls or frequency
optional arguments:
-h, --help show this help message and exit
-v, --version Print version and exit.
-m, --methylation METHYLATION [METHYLATION ...]
data in nanopolish, nanocompore, ont-cram or bedgraph
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
-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 tracks
--static Make a static image of the browser window (filename)
--binary Make the nanopolish plot ignorning log likelihood nuances
--smooth Rolling window size for averaging frequency values (int)
--dotsize Control the size of dots in the per read plots (int)
--example Show example command and exit.
-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_methyl
ation_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
Code Snippets
35 36 37 38 39 | shell: """ nanopolish index -d {input.f5}/ {input.fq} 2> {log} touch {output} """ |
54 55 56 57 58 59 60 61 62 | shell: """ nanopolish call-methylation \ -t {threads} \ -r {input.fq} \ -b {input.bam} \ -g {input.genome} \ -w {params.region} > {output} 2> {log} """ |
73 74 75 76 | shell: """ python {params.script} -i {input} > {output} 2> {log} """ |
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