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bio-methylation-calling

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Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.

When to use

• Extract methylation calls from Bismark BAM
• Generate per-cytosine methylation reports
• Extract CpG, CHG, and CHH contexts
• Generate bedGraph files
• Generate genome-wide cytosine reports
• Generate M-bias plots
• Convert bedGraph to BigWig
• Parse output in Python

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