/nextflow-development

nf-core/atacseq

Version: 2.1.2

Official Documentation: https://nf-co.re/atacseq/2.1.2/ GitHub: https://github.com/nf-core/atacseq

Note: When updating to a new version, check the releases page for breaking changes and update the version in commands below.

Contents

• Test command
• Samplesheet format
• Parameters
• Output files
• Quality metrics

Test command

nextflow run nf-core/atacseq -r 2.1.2 -profile test,docker --outdir test_atacseq

Expected: ~15 min, creates peaks and BigWig tracks.

Samplesheet format

sample,fastq_1,fastq_2,replicate
CONTROL,/path/to/ctrl_rep1_R1.fq.gz,/path/to/ctrl_rep1_R2.fq.gz,1
CONTROL,/path/to/ctrl_rep2_R1.fq.gz,/path/to/ctrl_rep2_R2.fq.gz,2
TREATMENT,/path/to/treat_rep1_R1.fq.gz,/path/to/treat_rep1_R2.fq.gz,1
TREATMENT,/path/to/treat_rep2_R1.fq.gz,/path/to/treat_rep2_R2.fq.gz,2

Design file for differential analysis

sample,condition
CONTROL,control
TREATMENT,treatment

Use with --deseq2_design design.csv.

Parameters

Minimal run

nextflow run nf-core/atacseq -r 2.1.2 -profile docker \
    --input samplesheet.csv --outdir results --genome GRCh38 --read_length 50

Common parameters

Differential accessibility

--deseq2_design design.csv

Output files

results/
├── bwa/mergedLibrary/
│   ├── *.mLb.mkD.sorted.bam     # Filtered, deduplicated alignments
│   └── bigwig/
│       └── *.bigWig             # Coverage tracks
├── macs2/narrowPeak/
│   ├── *.narrowPeak             # Peak calls
│   └── consensus/
│       └── consensus_peaks.bed  # Merged peaks across replicates
├── deeptools/
│   ├── plotFingerprint/         # Library complexity
│   └── plotProfile/             # TSS enrichment
├── deseq2/                      # If --deseq2_design provided
└── multiqc/

Key outputs:

• *.mLb.mkD.sorted.bam: Analysis-ready alignments
• *.narrowPeak: MACS2 peak calls (BED format)
• consensus_peaks.bed: Consensus peaks across replicates
• *.bigWig: Genome browser tracks

Quality metrics

Fragment size: Should show nucleosomal periodicity (~50bp nucleosome-free, ~200bp mono-nucleosome).

Downstream analysis

library(ChIPseeker)
library(GenomicRanges)
peaks <- import("consensus_peaks.bed")
peakAnno <- annotatePeak(peaks, TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene)

Motif analysis:

findMotifsGenome.pl consensus_peaks.bed hg38 motifs/ -size 200

Troubleshooting

Low FRiP: Check library complexity in plotFingerprint/. May indicate over-transposition.

Few peaks: Lower threshold with --macs_qvalue 0.1 or use --narrow_peak false for broader peaks.

High duplicates: Normal for low-input; pipeline removes by default.

More Information

• Full parameter list: https://nf-co.re/atacseq/2.1.2/parameters/
• Output documentation: https://nf-co.re/atacseq/2.1.2/docs/output/
• Usage documentation: https://nf-co.re/atacseq/2.1.2/docs/usage/