BioClaw atac-seq

ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.

install

source · Clone the upstream repo

git clone https://github.com/Runchuan-BU/BioClaw

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/Runchuan-BU/BioClaw "$T" && mkdir -p ~/.claude/skills && cp -r "$T/container/skills/atac-seq" ~/.claude/skills/runchuan-bu-bioclaw-atac-seq && rm -rf "$T"

manifest: container/skills/atac-seq/SKILL.md

source content

ATAC Seq

Version Compatibility

Reference examples assume:

```
macs3
```
3.0+
```
samtools
```
1.18+
```
deepTools
```
3.5+

Verify the runtime first:

CLI:

macs3 --version

samtools --version

bamCoverage --version

Overview

Use this skill when the user needs:

bulk ATAC-seq QC
peak calling
accessibility counting
differential accessibility
motif deviation or footprint follow-up

When To Use This Skill

the task is bulk ATAC-seq rather than ChIP-seq
TSS enrichment, fragment periodicity, or FRiP need review
the output should include peaks, counts, and downstream accessibility summaries

Quick Route

paired-end bulk ATAC: use
```
BAMPE
```
call peaks without control using ATAC-specific settings
if TSS enrichment is poor, stop and flag data quality before interpretation

Progressive Disclosure

Read technical_reference.md for QC gates and assay-specific caveats.
Read commands_and_thresholds.md for peak-calling commands, thresholds, and output conventions.

Prerequisites

Check Guidance

uniquely mapped reads

>= 20M

preferred for strong bulk ATAC

TSS enrichment

> 7

acceptable,

> 10

strong

FRiP

> 0.2

often strong for good bulk ATAC

Expected Inputs

paired-end ATAC BAM or FASTQ
reference genome
sample groups for comparisons

Expected Outputs

```
results/peaks/sample_peaks.narrowPeak
```

results/matrix/consensus_peak_counts.tsv

```
results/diff_accessibility.tsv
```
```
figures/tss_enrichment.pdf
```
```
figures/fragment_size_distribution.pdf
```

Starter Pattern

macs3 callpeak \
  -t atac.bam \
  -f BAMPE \
  -g hs \
  -n sample \
  --nomodel \
  --shift -100 \
  --extsize 200 \
  -q 0.01 \
  --outdir results/peaks

Key Parameters

Parameter	Typical value	Notes
`-f`	`BAMPE`	paired-end ATAC should use fragment-aware mode
`--nomodel`	on	standard for ATAC
`--shift`	`-100`	common Tn5 offset convention
`--extsize`	`200`	common first-pass extension
`-q`	`0.01`	starting FDR threshold

Workflow

1. Validate assay QC

Review:

TSS enrichment
fragment size periodicity
duplication
mapped read depth

2. Call peaks with ATAC-specific settings

Use fragment-aware paired-end mode and Tn5-aware shifting or equivalent settings.

3. Build a consensus peak matrix

Merge peaks across samples, count fragments into consensus intervals, then produce a peak-by-sample matrix.

4. Test differential accessibility

Use replicate-aware statistics and report both effect size and adjusted significance.

5. Run motif or footprint follow-up

Only after peak quality and read depth support it.

Output Artifacts

results/
├── peaks/
│   ├── sample_peaks.narrowPeak
│   └── sample_summits.bed
├── matrix/
│   └── consensus_peak_counts.tsv
└── diff_accessibility.tsv
qc/
├── tss_enrichment.tsv
└── fragment_metrics.tsv
figures/
├── tss_enrichment.pdf
└── fragment_size_distribution.pdf

Quality Review

TSS enrichment below
```
7
```
should trigger caution.
Strong nucleosome periodicity supports a good bulk ATAC library.
FRiP below
```
0.1
```
is usually weak and needs scrutiny.
Footprinting should not be trusted on low-depth or poor-quality libraries.

Anti-Patterns

using generic ChIP peak-calling defaults for ATAC
running footprinting on weak libraries
skipping TSS enrichment review
merging peaks from mixed reference builds

Related Skills

ChIP Seq
Gene Regulatory Networks
Multiome And scATAC

Optional Supplements

```
deeptools
```
```
pysam
```