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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger multi: Summary Metrics

cellranger multi supports a number of library types from the same experiment, including Gene Expression, VDJ T, VDJ B, and Cell Surface Protein Capture.

In order to organize output metrics resulting from multiple libraries and multiple samples, the metrics_summary.csv file has one metric per row and the following columns:

Column Name Description
Category Categorized the metric based whether it applies to only cell-associated barcodes (Cells) or to the whole library (Library). This distinction corresponds to whether a metric is found in the "Library" or "Cell" view of the cellranger multi web summary.
Library Type Either Gene Expression, VDJ T, VDJ B, Antigen Capture, Antibody Capture, or CRISPR.
Grouped By Describes the categories that a metric may describe/group by. Example categories are Physical library ID, Fastq ID.
Group Name The name of the Grouped By category. Example: GEX_1 (a physical library ID), Seq_GEX_1 (a fastq ID), GRCh38 (a genome name), etc.
Metric Name The name of the metric.
Metric Value The value of the metric.

Refer to the multi pipeline page to learn about running cellranger multi. To continue learning about multi outputs, visit the Filtered Outputs page.