barcode-fragment-mapping

barcode-fragment-mapping

Summary

Convert coordinate-sorted BAM files into compressed fragment files with cell barcode and quality annotations using SnapATAC2's pp.make_fragment_file. This preprocessing step is essential for single-cell ATAC-seq analysis, enabling efficient storage and downstream processing of chromatin accessibility data.

When to use

You have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including cell barcodes, fragment coordinates, and quality metrics for downstream analysis in SnapATAC2 or compatible tools.

When NOT to use

• Input BAM file is not coordinate-sorted; use samtools sort to order by chromosome and position first.
• Fragment file already exists in validated BED.gz or zst format; re-processing is redundant.
• Data source is unstranded or non-ATAC-seq (e.g., whole-genome bisulfite sequencing); barcode-fragment mapping assumes paired-end ATAC-seq reads with valid cell barcodes.

Inputs

• coordinate-sorted BAM file
• 10X Genomics BAM file (optional source specification)

Outputs

• compressed fragment file (BED.gz or .zst format)
• fragment metadata with barcode annotations
• QC metrics (duplication rate, read count)

How to apply

Load the coordinate-sorted BAM file and invoke pp.make_fragment_file with source='10x' if processing 10X BAM input, or with default settings for standard BAM files. The function generates a compressed fragment file (BED.gz or zst format) containing canonical BED fields (chrom, start, end) plus barcode and count columns. After execution, validate output file integrity by confirming non-empty content, verifying BED format compliance, and checking that QC metrics (duplication rate, read counts) are computed and accessible via the output metadata. The compressed output enables scalable processing of large cell numbers while preserving fragment-level information needed for tile matrix construction and peak calling.