Question: Does cellranger-atac aggr redo peak calling?
Answer: Yes, cellranger-atac aggr pipeline redo peak calling while preserving the same sets of barcodes identified as cells from cellranger-atac count analysis.
First, we combine all the fragments from all the input libraries (optionally with depth normalization). Then we rerun the peak-calling algorithm using all the fragments while retaining the same cell barcodes from cellranger-atac count.
Relevant support documentation: Cell Ranger ATAC aggr pipeline