prepare-atac

Linux CLI or Linux container only. Download public ATAC-seq reads or use local FASTQ files, then trim, align, filter, call peaks, calculate alignment coverage, and write QC files. The GUI and native macOS/Windows installations start from filtered BAM/BAI and peak BED files.

Example command

prepare-atac --samples metadata.tsv --genome hg38 --outdir project

Primary inputs

• --samples — TSV or CSV sample sheet containing sample, condition, and either paired fastq_1/fastq_2 paths or URLs. See the bulk workflow guide.
• --genome — packaged hg38 or mm10 reference label, or a custom label used with explicit reference options.
• --outdir — project directory represented by {project} below.

Repeated rows with the same sample, condition, and replicate combine technical sequencing runs. Different sample values sharing a condition are biological replicates.

Main outputs

For each {sample}, the default modern profile writes:

Path	Meaning
{project}/samples/{sample}/alignment/{sample}.filtered.bam	Coordinate-sorted, filtered ATAC-seq alignment used downstream.
{project}/samples/{sample}/alignment/{sample}.filtered.bam.bai	Samtools index for the filtered BAM.
{project}/samples/{sample}/peaks/{sample}.narrowPeak	MACS3 narrow-peak calls before project-level merging.
{project}/samples/{sample}/tracks/{sample}.rp10m.bw	Sequencing-depth-normalized alignment coverage bigWig. rp10m is retained only as the historical filename suffix.
{project}/samples/{sample}/qc/{sample}.fastp.html	Interactive Fastp read-trimming QC report.
{project}/samples/{sample}/qc/{sample}.fastp.json	Machine-readable Fastp metrics.
{project}/samples/{sample}/qc/flagstat.tsv	Samtools alignment and filtering counts.
{project}/samples/{sample}/qc/fragment_lengths.tsv	Fragment-length distribution used to inspect ATAC-seq periodicity.
{project}/samples/{sample}/qc/metrics.json	Consolidated per-sample QC metrics.
{project}/samples/{sample}/qc/commands.log	External commands used for that sample.

Project-level files include:

Path	Meaning
{project}/peaks/merged_peaks.bed	Union of sample peak intervals.
{project}/peaks/merged_peaks_filtered.bed	Analysis peak set after excluded chromosomes are removed.
{project}/metadata/resolved_runs.tsv	Resolved local/downloaded FASTQ files and run grouping.
{project}/metadata/samples.tsv	Downstream sample, condition, bam, and peaks table accepted by core commands.
{project}/reports/qc_summary.tsv	Cross-sample QC summary.

Continue with atac-correct, or see the complete prepare-atac reference.