chromatin-accessibility-quantification

chromatin-accessibility-quantification

Summary

Quantify chromatin accessibility across the genome at fixed genomic intervals (tiles) from single-cell ATAC-seq fragment data using SnapATAC2's paired-insertion counting strategy. This skill converts aligned fragment coordinates and cell barcodes into a sparse count matrix suitable for downstream analysis.

When to use

You have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .obsm['fragment_single']) from aligned single-cell ATAC-seq data and need to generate a tile-based count matrix to quantify chromatin accessibility for clustering, embedding, or peak discovery.

When NOT to use

• Fragment data has not yet been loaded or parsed into the AnnData object—use pp.import_fragments or pp.make_fragment_file first.
• You require peak-level counts instead of fixed-interval tiles—use pp.make_peak_matrix instead.
• Input is already a pre-computed feature matrix; tiling and counting would be redundant.

Inputs

• Backed AnnData object with fragment data in .obsm['fragment_paired'] or .obsm['fragment_single']
• Cell barcodes (stored in .obs)
• Fragment coordinates (chromosome, start, end) and quality metrics

Outputs

• Tile-based count matrix (n_obs × n_vars, sparse format)
• Tile coordinate metadata (genomic positions of each bin)
• QC metrics (fragment counts per cell, sparsity)

How to apply

Load your backed AnnData object containing pre-parsed fragment data. Invoke pp.add_tile_matrix with counting_strategy='paired_insertion' to assign each fragment pair to fixed genomic tiles (default tile size is typically 5 kb) and count the number of fragments per tile per cell. The function scans all fragments, maps their coordinates to tile bins, and aggregates counts by cell barcode and tile ID. Verify that the resulting count matrix has shape (n_obs × n_vars) matching the number of cells and tiles, and confirm non-zero entries are distributed across both cells and genomic regions, indicating successful quantification.