Tn5-based chromatin footprinting and regulatory motif analysis¶
fp-tools provides command-line and browser workflows for bulk and single-cell
footprinting of Tn5-based chromatin profiling data, including ATAC-seq,
CUT&Tag, and related assays. It connects bias correction, footprint scoring,
motif analysis, replicate comparisons, and reusable reports.
- Analyze aligned Tn5-based chromatin data from BAM and peak files.
- Compare motif-associated footprint scores across samples and replicates.
- Analyze pseudobulk and per-cell footprint signatures.
- Export static figures and portable interactive HTML reports.
Choose your starting point:
- BAM/BAI and peak BED files: follow the runnable bulk ATAC-seq workflow.
- Single-cell fragments: follow the single-cell workflow.
- Existing fp-tools outputs: open the output demo or choose a command in the tool overview.
Linux command-line and container users can optionally prepare FASTQ files with
prepare-atac.