Cell Ranger6.0, printed on 06/09/2023
This page describes the differences between the metrics_summary.csv generated by cellranger count and cellranger multi.
The metrics_summary.csv is organized with each column specifying one metric name. The metric values are specified in a single row below.
cellranger multi supports a number of library types from the same experiment, including Gene Expression, Multiplexing Capture, VDJ T, VDJ B, Antibody Capture, CRISPR Guide Capture, and Custom (user-defined assays). cellranger multi also produces some results that are per-sample (only calculated over reads from barcodes assigned to a specific multiplexed sample), as well as others that are per-library (calculated over all reads from that library). In order to organize output metrics resulting from multiple libraries and multiple samples, the metrics summary CSV has one metric per row. The CSV has the following columns: