MethGo

MethGo analyzes bisulfite sequencing (BS-Seq) data from whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) to profile DNA cytosine methylation at single-base resolution from bisulfite-converted next-generation sequencing data for epigenomic studies.

Key Features:

• Coverage distribution: Computes per-cytosine coverage distribution across BS-Seq data.
• Global cytosine methylation levels: Quantifies overall cytosine methylation levels genome-wide.
• Genome-wide methylation distribution: Profiles distribution patterns of cytosine methylation across the genome.
• Element-specific methylation profiling: Reports cytosine methylation levels within defined genomic regions.
• Chromosome-wide distribution: Calculates methylation distribution at the chromosome scale.
• Gene-centric analysis: Determines methylation levels associated with genes.
• Transcription factor binding site (TFBS) methylation: Assesses methylation patterns surrounding TFBSs.
• Genetic variation analysis: Performs single nucleotide polymorphism (SNP) calling and copy number variation (CNV) calling.

Scientific Applications:

• Epigenetic profiling: Characterizes global and locus-specific DNA methylation landscapes from WGBS and RRBS.
• Gene regulation studies: Investigates methylation patterns around TFBSs to inform regulatory mechanism analyses.
• Disease and developmental research: Compares methylation profiles associated with disease states and developmental stages.
• Integrative genomics: Links methylation data with SNPs and CNVs to study interactions between genetic variation and epigenetic modifications.

Methodology:

Computational steps explicitly include computing per-cytosine coverage distributions, calculating global cytosine methylation levels, profiling methylation distribution across genome regions and chromosomes, performing gene-centric methylation analysis, assessing methylation around TFBSs, and calling SNPs and CNVs.