Tool overview

The guides below cover common inputs and outputs. See the API Reference for every option.

If you are new to fp-tools, start with the bulk ATAC-seq workflow: it includes a BAM/peak sample sheet, an explicit comparison table, ENCODE downloads, and the expected output layout. Optional Linux-only FASTQ preprocessing is kept separate under prepare-atac.

Core analysis

• atac-correct — correct ATAC-seq cut-site signal for Tn5 sequence bias.
• call-footprints — calculate footprint-score tracks from corrected signal.
• match-motifs — scan motifs and summarize motif-associated footprint scores.
• diff-footprints — compare conditions or user-defined region sets, with replicate-aware statistics.
• normalize-bigwig — normalize corrected cut-site signals over shared background regions.

Visualization and review

• plot-aggregate — plot signal around motif sites or user-defined BED regions; also export motif-by-comparison PDF grids.
• review-multi-comparisons — combine differential reports into one static comparison browser.

Workflow and interface

• bulk-footprinting — run the complete bulk workflow from BAM/BAI and peak BED inputs.
• sc-footprinting — run pseudobulk and per-cell single-cell ATAC-seq footprinting.
• run-yaml-workflow — run command-compatible jobs from YAML.
• fp-tools-gui — launch the browser interface.
• fp-tools-runtime — inspect or prepare the managed external-tool runtime.

Linux preprocessing

• prepare-atac — prepare FASTQ inputs as filtered BAM, peak, alignment coverage, and QC outputs from the Linux CLI or Linux container.

De Novo Motif Discovery

• discover-motifs — discover motifs from footprint candidates.
• summarize-motifs — summarize discovered motifs and known-motif matches.

Single-cell ATAC-seq utilities

• pseudobulk-fragments — group fragments by cell annotation.
• find-signature-fp — plot per-cell footprint-signature heatmaps and UMAPs.