pseudobulk-fragments

Group single-cell ATAC fragments by a cell-annotation column to create pseudobulk inputs.

Example command

pseudobulk-fragments --fragments pbmc_fragments.tsv.gz --annotations cell_annotations.tsv --group-by cell_type \
  --genome-sizes hg38.chrom.sizes --write-cutsite-bigwigs --outdir project/pseudobulk/fragments

Primary inputs

• --fragments — single-cell fragment TSV or TSV.GZ file.
• --annotations — barcode-level cell annotation table.
• --group-by — annotation column used to define pseudobulk groups.
• --genome-sizes — chromosome sizes used to write signal tracks.
• --write-cutsite-bigwigs — write cut-site bigWigs for retained groups.
• --outdir — directory for grouped fragments, tracks, and QC outputs.

Main outputs

For each sanitized {group} under {outdir}:

Path	Meaning
{group}.fragments.tsv or {group}.fragments.tsv.gz	Fragments assigned to the group; compressed/indexed form is controlled by the command options.
{group}.fragments.tsv.gz.tbi	Optional Tabix index for random genomic access.
{group}.cutsites.cpm.bw	Optional CPM-normalized cut-site signal bigWig written by --write-cutsite-bigwigs.
{group}.pseudo_pairs.sorted.bam and .bai	Optional pseudo-paired alignment used by atac-correct with read shift 0 0.
pseudobulk_manifest.tsv	Per-group paths, cell/fragment counts, and filter status.
fp_tools_manifest.yml	Machine-readable run settings and retained groups.
pseudobulk_downstream_commands.sh	Optional generated downstream command examples.

Continue with sc-footprinting, or see the complete pseudobulk-fragments reference.