msgbsR

msgbsR analyzes methylation-sensitive restriction enzyme sequencing data (MRE-seq), including genotyping-by-sequencing (GBS) and RAD-seq, to identify and quantify DNA methylation signals from BAM alignments using read-coverage-based metrics for differential methylation analysis.

Key Features:

• Methylation-sensitive enzyme analysis: Tailored for experiments using methylation-sensitive restriction enzymes and applicable to MRE-seq workflows combined with GBS or RAD-seq.
• Alignment file processing (BAM): Parses BAM alignment files to identify and quantify read counts at putative methylation-sensitive restriction sites.
• Enzyme cut-site verification: Verifies that observed restriction enzyme cut sites match the expected recognition sequences for individual enzymes.
• Read-coverage-based methylation assessment: Assesses DNA methylation using read coverage (analogous to RNA-seq count-based approaches) rather than proportion-based methylation measures.
• Population- and large-genome support: Enables differential methylation analysis across large populations and genomes with high genetic diversity.
• R package implementation: Implemented as an R package to perform the described computational analyses.

Scientific Applications:

• Epigenetic studies: Analysis of DNA methylation dynamics and locus-specific methylation patterns from restriction enzyme sequencing assays.
• Population genetics: Population-scale differential methylation analysis across many individuals and genetically diverse species.
• Comparative genomics: Comparative examination of methylation patterns across genomes or populations, including unannotated genomic regions.
• Gene regulation and environmental studies: Investigation of methylation-linked regulation related to development, gene expression, and environmental effects.

Methodology:

Parses BAM alignments to count reads at restriction enzyme cut sites, verifies recognition sequences for enzymes, and uses read-coverage-based quantification (analogous to RNA-seq counts) to support differential methylation analysis of MRE-seq/GBS/RAD-seq data.