Single-cell ATAC-seq workflow

sc-footprinting groups fragments into pseudobulk samples, runs the footprint analysis, and calculates per-cell footprint signatures.

Main commands

sc-footprinting

• sc-footprinting runs the complete workflow.
• pseudobulk-fragments and find-signature-fp remain available as focused utilities.

Example

sc-footprinting --fragments 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

See the Single-cell output example.