Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-methylation-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-methylation-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinextract

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-methylation-calling

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: bismark_methylation_extractor --bedGraph --cytosine_report sample.bam.
Extract methylation calls from my Bismark BAM" → Generate per-cytosine methylation reports (CpG, CHG, CHH contexts) from aligned bisulfite sequencing data. CLI: bismark_methylation_extractor --bedGraph --cytosine_report sample.bam.
bismark_methylation_extractor --gzip --bedGraph \ sample_bismark_bt2.bam.

Source Doc

Excerpt From SKILL.md

Most common - extract only CpG methylation

bismark_methylation_extractor
--paired-end
--no_overlap \ # Avoid double counting overlapping reads --gzip
--bedGraph
--CX \ # Also extract CHG/CHH (optional) sample.bam


## Comprehensive report with all CpGs in genome

bismark_methylation_extractor \
    --paired-end \
    --gzip \
    --bedGraph \
    --cytosine_report \
    --genome_folder /path/to/genome/ \
    sample.bam