bio-workflows-atacseq-pipeline
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.
npx skills add BioTender-max/awesome-bio-agent-skills --skill atacseq-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: Bowtie2 2.5.3+, MACS3 3.0+, bedtools 2.31+, deepTools 3.5+, fastp 0.23+, samtools 1.19+ 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. # ATAC-seq Pipeline **"Run end-to-end ATAC-seq analysis from FASTQ to differential accessibility"** → Orchestrate QC, Bowtie2 alignment, MACS3 peak calling, FRiP/TSS enrichment QC, differential accessibility, and optional TOBIAS footprinting. Complete workflow from raw ATAC-seq FASTQ files to accessibility peaks, differential analysis, and TF footprinting. ## Workflow Overview ``` FASTQ files | v [1. QC & Trimming] -----> fastp (Nextera adapters) | v [2. Alignment] ---------> Bowtie2 | v [3. BAM Processing] ----> filter, shift, dedup | v [4. Peak Calling] ------> MACS3 | v [5. QC] ----------------> TSS enrichment, FRiP, fragment size | v [6. Differential] ------> DiffB
- Version Compatibility
- Workflow Overview
- Primary Path: Bowtie2 + MACS3
- Step 1: Quality Control with fastp
- Step 2: Alignment with Bowtie2
- Step 3: BAM Processing
- Step 4: Peak Calling with MACS3
- Step 5: ATAC-seq QC
- Step 6: Differential Accessibility with DiffBind
- Step 7: TF Footprinting with TOBIAS
- Parameter Recommendations
- Troubleshooting
- Complete Pipeline Script
- Related Skills
ATAC-seq uses Nextera adapters
for sample in sample1 sample2 sample3; do
fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \
done
Build index (once)
bowtie2-build genome.fa bt2_index/genome
Align with ATAC-seq specific settings
bowtie2 -p 8 -x bt2_index/genome \
samtools view -@ 4 -bS -q 30 -f 2 - | \
samtools sort -@ 4 -o aligned/${sample}.bamWhat does the bio-workflows-atacseq-pipeline skill do?
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential accessibility.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill atacseq-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.