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Metrics Output from the Cell Ranger multi Pipeline

Metrics Output from the Cell Ranger multi Pipeline

Cell Ranger multi supports a number of library types from the same experiment, including Gene Expression, CRISPR, VDJ-T, VDJ-B, Antigen Capture (BEAM), and Antibody Capture (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 NameDescription
CategoryCategorized 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 TypeEither Gene Expression, VDJ T, VDJ B, Antigen Capture, Antibody Capture, or CRISPR.
Grouped ByDescribes the categories that a metric may describe/group by. Example categories are Physical library ID, Fastq ID.
Group NameThe 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 NameThe name of the metric.
Metric ValueThe value of the metric.

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