DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
Project description
Full documentation is available at https://a-slide.github.io/pycoMeth/
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
pycoMeth
can be used for further analyses starting from the output files generated by Nanopolish call-methylation
. The package contains a suite of tools to find CpG islands calculate the methylation probability at CpG dinucleotide or CpG island resolution across the entire genome and to perform a simple differential methylation analysis across multiple samples.
pycoMeth
generates extensive tabulated reports and BED files which can be loaded in a genome browser. In addition, an interactive HTML report of differentially
methylated intervals/islands can also generated at the end of the analysis.
Methplotlib
developed by Wouter de coster is an excellent complementary tool to visualise and explore methylation status for specific loci.
Please be aware that pycoMeth
is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
pycoMeth workflow
pycoMeth example output IGV rendering
pycoMeth example HTML report
Citing
The repository is archived at Zenodo. If you use pycoMeth
please cite as follow:
Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254
Authors and contributors
- Adrien Leger (@a-slide) - aleg {at} ebi.ac.uk
Project details
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