Question: Does the Cell Ranger ATAC pipeline use static thresholds to call peaks and identify cell barcodes?
Answer: No. For each library, the pipeline dynamically computes the most appropriate peak-calling threshold and cell-calling threshold based on available sequencing and mapping data. All other things being equal, a library with fewer cells or lower sequencing coverage will generally also have lower thresholds.
For more information on this topic, please consult the peak-calling and cell-calling documentation page.