数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-methylation-calling

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-methylation-calling🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinextract

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

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

原始文档

SKILL.md 摘录

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

Merge strands (CpG methylation is usually symmetric)

bismark_methylation_extractor --merge_non_CpG --gzip sample.bam

适用场景

适合在extracting methylation levels ，面向 aligned bisulfite sequencing data ，用于 downstream analysis时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

bismark-alignment - Generate input BAM files
methylkit-analysis - Import coverage files to R
dmr-detection - Find differentially methylated regions

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