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Tool overview

Choose a command by the task you want to perform. Each guide explains its inputs, gives an example command, and lists the files it writes. See the Command reference for all command options.

If you are new to fp-tools, start with the bulk ATAC-seq workflow: it includes minimal sample and comparison tables and explains where to find your results. For fragments and cell annotations, use the single-cell workflow. Linux users starting from FASTQ files can prepare BAM and peak files with prepare-atac first.

Core analysis

Examples in command guides are templates: replace input paths with your files and run from the folder containing those paths. Output paths are relative to that same working folder. For a complete analysis, follow a workflow guide, then use each command's “Main outputs” section to locate the result.

  • 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 saved command settings from a YAML file.
  • fp-tools-gui — launch the browser interface.
  • fp-tools-runtime — check or install the external tools used for read preparation and motif discovery.

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

Single-cell ATAC-seq utilities

Practical glossary

Term Meaning in this guide
GUI Graphical user interface: forms and buttons for setting up analyses.
CLI Command-line interface: commands entered in a terminal.
YAML YAML Ain't Markup Language: a text format used to save analysis settings and paths.
BAM / BAI Binary alignment/map file containing aligned reads, and its matching index for efficient access.
BED Browser extensible data: genomic intervals, with zero-based starts and end positions excluded.
bigWig A genome-wide numerical signal track.
FASTA A sequence-file format; reference DNA must match your inputs' genome assembly.
AnnData / h5ad Annotated data stored in an HDF5 file; single-cell analysis needs matching barcodes and genomic-bin counts.
Pseudobulk Fragments combined from cells in the same annotated group.
KNN smoothing K-nearest-neighbor smoothing: combining information from nearby cells to reduce sparse measurements.
UMAP Uniform manifold approximation and projection: a low-dimensional view of similarities between cells.
TF Transcription factor; a motif match alone does not establish which protein is bound.
FDR False discovery rate: the expected proportion of false discoveries among selected statistical results.
DWM Dinucleotide weight matrix: the sequence-bias model used by the default correction.
Managed runtime Supporting analysis programs that fp-tools downloads and prepares when needed.

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