atac-correct

Estimate Tn5 sequence bias from aligned ATAC-seq fragments and subtract the expected bias contribution from the observed cut-site signal. Run this before footprint scoring.

Example command

atac-correct --sample-table project/metadata/samples.tsv --genome hg38.fa.gz --blacklist hg38.blacklist.bed --outdir project

Primary inputs

• --sample-table — TSV with sample, condition, bam, and peaks; BAM indexes must be adjacent to the BAMs.
• --genome — reference FASTA whose chromosome names and assembly match every BAM and peak BED.
• --blacklist — BED intervals excluded from bias estimation and corrected output.
• --outdir — project directory represented by {project} below.

Main outputs

For each {sample}, project layout writes:

Path	Meaning
{project}/samples/{sample}/atac_correct/{sample}_corrected.bw	Bias-corrected cut-site signal. Positive positions have more observed cuts than expected; negative positions have fewer.
{project}/samples/{sample}/atac_correct/{sample}_atacorrect.pdf	Diagnostic plots comparing learned Tn5 sequence bias before and after correction. Omitted with --skip-qc.
{project}/samples/{sample}/atac_correct/{sample}_AtacBias.pickle	Serialized learned bias model for reuse or advanced debugging. It is not required by downstream commands.

With --write-tracks all, the same directory also contains:

Path	Meaning
{sample}_uncorrected.bw	Observed base-resolution cut-site signal after the configured forward/reverse read shifts and sequencing-depth normalization.
{sample}_bias.bw	Tn5 sequence-bias score predicted from the reference sequence.
{sample}_expected.bw	Expected cut-site signal after the sequence-bias score is scaled to local observed cuts.

Project-level peak outputs are {project}/peaks/merged_peaks.bed and {project}/peaks/merged_peaks_filtered.bed. A direct single-BAM run writes the same {prefix}_*.bw, {prefix}_atacorrect.pdf, and {prefix}_AtacBias.pickle patterns directly under {outdir}.

Open a representative ENCODE ATACCorrect PDF. Continue with call-footprints, or see the complete atac-correct reference.