10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger6.0, printed on 12/21/2024

Metrics Summary CSV

This page describes the differences between the metrics_summary.csv generated by cellranger count and cellranger multi.

cellranger count

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

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:

1. Library or Sample : whether the metric applies to only the barcodes from the (possibly multiplexed) sample or to the whole library. This distinction corresponds to whether a metric is found in the "Library" or "Sample" view of the cellranger multi web summary.
2. Library Type : either Gene Expression, Multiplexing Capture, VDJ T, VDJ B, Antibody Capture, CRISPR Guide Capture, or Custom
3. Grouped By: this describes categories that a metric may describe/group over. For example, "Physical library ID", "Fastq ID", "Genome", or "CMO Name"
4. Group Name: the name of the "Grouped By" category. For example, "GEX_1" (a physical library ID), "Seq_GEX_1" (a fastq ID), "GRCh38" (a genome name), "CMO301" (a CMO name) etc
5. Metric Name: the name of the metric
6. Metric Value: the value of the metric