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cvlr: finding heterogeneously methylated genomic regions using ONT reads.
Raineri, Emanuele; Alberola I Pla, Mariona; Dabad, Marc; Heath, Simon.
Affiliation
  • Raineri E; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
  • Alberola I Pla M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
  • Dabad M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
  • Heath S; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.
Bioinform Adv ; 3(1): vbac101, 2023.
Article in En | MEDLINE | ID: mdl-36726731
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.

Full text: 1 Collection: 01-internacional Database: MEDLINE Type of study: Diagnostic_studies Language: En Journal: Bioinform Adv Year: 2023 Document type: Article Affiliation country: Country of publication:

Full text: 1 Collection: 01-internacional Database: MEDLINE Type of study: Diagnostic_studies Language: En Journal: Bioinform Adv Year: 2023 Document type: Article Affiliation country: Country of publication: