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 BioTender-max/awesome-bio-agent-skills --skill methylation-calling --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.
## Version Compatibility Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Methylation Calling **"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` ## 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
- Version Compatibility
- 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
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 BioTender-max/awesome-bio-agent-skills --skill methylation-calling --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.