atac-correct

Correct ATAC-seq cut-site signal for Tn5 sequence bias. Start with coordinate-sorted BAM files, adjacent BAI indexes, and matching peak BED files. Use the corrected signal as the input to call-footprints.

Example command

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

Primary inputs

• --sample-table — tab-separated file with one row per sample and the columns sample, condition, bam, and peaks. Give each sample a unique name and use the same condition label for biological replicates.
• --genome — reference FASTA whose chromosome names and assembly match every BAM and peak BED.
• --blacklist — optional assembly-matched BED of regions to exclude from bias estimation and corrected output.
• --outdir — project directory represented by {project} below.

Use the sample-table example to prepare your inputs. Replace the FASTA and blacklist paths with your own files. A custom FASTA does not automatically select a blacklist.

Main outputs

For each {sample} in the table, this command 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	Saved bias model for reuse. Downstream commands use the corrected bigWig and do not need this file.

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 the QC PDF to inspect the sequence-bias diagnostics, then use the corrected bigWig for footprint scoring. A negative corrected value means fewer cuts than the bias model expected; it does not by itself identify a bound TF.

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