bio-workflows-methylation-pipeline
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill methylation-pipeline --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: Bismark 0.24+, Bowtie2 2.5.3+, FastQC 0.12+, Trim Galore 0.6.10+, fastp 0.23+, methylKit 1.28+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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 Pipeline **"Analyze my bisulfite sequencing data from FASTQ to DMRs"** → Orchestrate Bismark alignment, methylation calling, methylKit analysis, DMR detection, annotation with genomic features, and visualization of methylation patterns. Complete workflow from bisulfite sequencing FASTQ to differentially methylated regions. ## Workflow Overview ``` FASTQ files | v [1. QC & Trimming] -----> fastp/Trim Galore | v [2. Alignment] ---------> Bismark | v [3. Deduplication] -----> deduplicate_bismark | v [4. Methylation Calling] -> bismark_methylation_extractor | v [5. Per-CpG Analysis] ---> methylKit (R) or scipy (Python) | v [6. DMR Detection] ------> me
- Version Compatibility
- Workflow Overview
- Primary Path: Bismark + methylKit
- Step 1: Quality Control
- Step 2: Bismark Alignment
- Step 3: Deduplication
- Step 4: Methylation Calling
- Step 5: Analysis with methylKit
- Step 5b: Python Alternative for Per-CpG Testing
- Step 6: DMR Detection
- Parameter Recommendations
- Troubleshooting
- Complete Pipeline Script
- Related Skills
Trim Galore recommended for bisulfite data (handles adapter bias) trim_galore --paired --fastqc \ sample_R1.fastq.gz sample_R2.fastq.gz Or fastp with conservative settings fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \ Prepare genome (once) bismark_genome_preparation --bowtie2 genome/ Align bismark --genome genome/ \ deduplicate_bismark \
What does the bio-workflows-methylation-pipeline skill do?
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill methylation-pipeline --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.