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sc-footprinting

Run grouping, bias correction, footprint scoring, motif analysis, and per-cell signature reporting for single-cell ATAC-seq data.

Example command

sc-footprinting --fragments pbmc_fragments.tsv.gz --annotations cell_annotations.tsv --h5ad cell_embedding.h5ad \
  --group-by cell_type --genome-sizes hg38.chrom.sizes --genome hg38.fa.gz --peaks merged_peaks.bed \
  --motif-db jaspar2026_vertebrates --outdir project/pseudobulk

Primary inputs

  • --fragments — single-cell fragment file.
  • --annotations — barcode-level cell annotation table.
  • --h5ad — AnnData file containing the cell embedding used for KNN smoothing.
  • --group-by — annotation column used to define pseudobulk groups.
  • --genome-sizes — chromosome sizes used to write grouped signal tracks.
  • --genome — reference genome FASTA.
  • --peaks — accessible-region BED file.
  • --motif-db — built-in motif database name.
  • --outdir — directory for pseudobulk tracks, motif results, and reports.

Main outputs

{outdir} contains a complete staged workflow:

Path Meaning
pseudobulk/{group}.fragments.tsv.gz and .tbi Indexed fragments for each retained cell group.
pseudobulk/{group}.cutsites.cpm.bw Group cut-site signal bigWig.
pseudobulk/{group}.pseudo_pairs.sorted.bam and .bai Pseudo-paired alignment used for bias correction.
atacorrect/{group}/{group}_corrected.bw Bias-corrected cut-site signal per group.
footprints/{group}_footprints.bw Footprint score signal per group.
diff_footprints/pseudobulk_diff_footprints_results.txt Optional motif-level group comparison results.
plots/single_cell_footprinting/ Per-cell score tables, heatmaps, and UMAP figures from find-signature-fp.
pseudobulk_footprint_manifest.tsv Group paths and workflow completion state.
pseudobulk_footprint_commands.sh Exact generated commands for reproducibility.
logs/{stage}.stdout.log and {stage}.stderr.log Captured output for each stage.

See the Single-cell workflow and the complete sc-footprinting reference.