bio-methylation-calling
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.
npx skills add majiayu000/claude-skill-registry --skill methylation-calling-gptomics-bioskills-2 --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Methylation Calling ## Basic Extraction ```bash # Extract methylation calls from Bismark BAM bismark_methylation_extractor --gzip --bedGraph \ sample_bismark_bt2.bam ``` ## Paired-End Extraction ```bash bismark_methylation_extractor --paired-end --gzip --bedGraph \ sample_bismark_bt2_pe.bam ``` ## Common Options ```bash bismark_methylation_extractor \ --paired-end \ # For paired-end data --gzip \ # Compress output --bedGraph \ # Generate bedGraph file --cytosine_report \ # Genome-wide cytosine report --genome_folder /path/to/genome/ \ # Required for cytosine_report --buffer_size 10G \ # Memory buffer --parallel 4 \ # Parallel extraction -o output_dir/ \ sample.bam ``` ## CpG Context Only ```bash # 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 ``` ## Genome-Wide Cytosine Report ```bash # Comprehensive report with all CpGs in genome bismark_methylation_extractor \ --paired-end \ --gzip \ --bedGraph \ --cytosine_report \ --genome_folder /path/to/genome/ \ sample.bam ``` ## Strand-Specific Output ```bash # Defau
- Basic Extraction
- Paired-End Extraction
- Common Options
- CpG Context Only
- Genome-Wide Cytosine Report
- Strand-Specific Output
- Avoid Double-Counting Overlapping Reads
- Generate Coverage File
- Convert to BigWig for Visualization
- M-Bias Plot
- Ignore End Bias
- Output Files
- Parse Output in Python
- Key Parameters
Extract methylation calls from Bismark BAM bismark_methylation_extractor --gzip --bedGraph \ sample_bismark_bt2.bam bismark_methylation_extractor --paired-end --gzip --bedGraph \ sample_bismark_bt2_pe.bam bismark_methylation_extractor \ sample.bam Most common - extract only CpG methylation Comprehensive report with all CpGs in genome CpG_OT_sample.txt - Original Top strand
What does the bio-methylation-calling skill do?
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.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill methylation-calling-gptomics-bioskills-2 --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.