Bismark Methylation Calling

What it does

This skill documents how to run bismark_methylation_extractor and related tools to produce per-cytosine methylation calls and coverage files from Bismark-aligned BAM inputs. It covers single- and paired-end extraction, common flags (gzip, bedGraph, cyotosine_report), options to handle overlapping reads, parallel extraction, M-bias analysis, and downstream conversions (bedGraph → BigWig). Examples and common parameter explanations are provided so users can generate genome-wide CpG/CHG/CHH reports suitable for visualization and downstream tools like methylKit.

When to use it

Use this skill when you have bisulfite-sequencing alignments produced by Bismark and need to extract methylation metrics for per-site analysis, QC (M-bias), visualization in genome browsers, or input into downstream differential methylation pipelines. It is intended for bioinformaticians preparing coverage/bedGraph files and CpG reports for analysis or archiving.

What's included

• Scripts: CLI example commands for basic extraction, paired-end handling, M-bias plots, and bedGraph to BigWig conversion. (has_scripts: false in repo but examples present in the SKILL.md body)
• References: Mentions related skills (alignment, methylkit, dmr detection) and file formats to expect.
• Instructions: Step-by-step CLI examples, recommended flags, and a short Python snippet showing how to parse coverage files into pandas for filtering.

Compatible agents

CLI-focused agents and bioinformatics automation runners (Shell/CLI-enabled agents, Codex/Gemini for documentation). The guidance is platform-agnostic and suitable for automation in pipelines or interactive runs.