Dataset Information

Cvlr: finding heterogeneously methylated genomic regions using ONT reads.

ABSTRACT:

Summary

Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous methylation. Our software can also compute the covariance of methylation across these regions while keeping into account the mixture of different types of reads.

Availability and implementation

https://github.com/EmanueleRaineri/cvlr.

Contact

simon.heath@cnag.crg.eu.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

SUBMITTER: Raineri E

PROVIDER: S-EPMC9887406 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

cvlr: finding heterogeneously methylated genomic regions using ONT reads.

Raineri Emanuele E Alberola I Pla Mariona M Dabad Marc M Heath Simon S

Bioinformatics advances 20230123 1

<h4>Summary</h4>Nanopore reads encode information on the methylation status of cytosines in CpG dinucleotides. The length of the reads makes it comparatively easy to look at patterns consisting of multiple loci; here, we exploit this property to search for regions where one can define subpopulations of molecules based on methylation patterns. As an example, we run our clustering algorithm on known imprinted genes; we also scan chromosome 15 looking for windows corresponding to heterogeneous meth ...[more]

PMID: 36726731

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