bulk-footprinting

Run bulk ATAC-seq from BAM/BAI and peak BED inputs through interactive reports.

The bulk workflow guide provides a runnable HepG2-versus-K562 ENCODE example.

Example command

bulk-footprinting --sample-table samples.tsv --comparison-table comparisons.tsv --genome hg38.fa.gz \
  --outdir project --cores 8

Primary inputs

• --sample-table — sample, condition, coordinate-sorted BAM, and peak BED columns.
• --comparison-table — comparison, condition 1, and condition 2 columns.
• --genome — reference FASTA matching the BAM and peak coordinates.
• --outdir — project output directory.
• --cores — total worker cores.

Main outputs

{project} is the --outdir, {sample} comes from the sample table, and {comparison} comes from the comparison table:

Path	Meaning
{project}/samples/{sample}/atac_correct/{sample}_corrected.bw	Bias-corrected cut-site signal.
{project}/samples/{sample}/footprints/{sample}_footprints.bw	Footprint score signal.
{project}/samples/{sample}/match_motifs/motif_matches_results.txt	Per-sample motif summary and binding calls.
{project}/comparisons/{comparison}/diff_footprints_results.txt	Motif-level differential statistics.
{project}/comparisons/{comparison}/diff_footprints_{cond1}_{cond2}.html	Portable interactive comparison report.
{project}/reports/review_multi_comparisons/index.html	Static browser combining every requested comparison.
{project}/reports/review_multi_comparisons.html	Aggregate-free portable review written when standalone HTML review mode is selected.
{project}/logs/bulk_footprinting/bulk_footprinting_commands.sh	Exact commands generated for the workflow stages.
{project}/logs/bulk_footprinting/{stage}.stdout.log and {stage}.stderr.log	Stage-specific logs for troubleshooting.

FASTQ preprocessing is intentionally separate. Linux users can run prepare-atac first, then provide its generated metadata/samples.tsv to this command.