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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

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
Library or Sample Whether the metric applies to only the barcodes from the 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.
Library Type Either Gene Expression, VDJ T, VDJ B, or Cell Surface Protein Capture.
Grouped By This describes categories that a metric may describe/group over. For example, "Physical library ID", "Fastq ID".
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), 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.