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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger7.0, printed on 11/14/2024

Web Summary: Cell Ranger Multi

Table of Contents

Web summary overview

The cellranger multi pipeline outputs an interactive summary HTML file named web_summary.html that contains summary metrics and automated secondary analysis results. If an issue was detected during the pipeline run, an alert appears on this page. More information about alerts is provided in the Cell Ranger troubleshooting documentation. The web_summary.html file is also the starting point for quality control on experiments run through cellranger multi, introduced in Cell Ranger 6.0.

The cellranger multi pipeline’s web summary has three views: Cells, Library, and Experimental Design:
  • Cells: Provides metrics, analysis, and visualization of data from cells called from this sample.
  • Library: Provides metrics, analysis, and visualization of data from each library generated in the experiment. In case the data is from a multiplexed experiment, please note that each library will contain cells assigned to different samples.
  • Experimental Design: Provides a visualization of the experimental design as inferred by Cell Ranger based on the CSV file provided by the user.

The web summary is interactive. Users can zoom in on specific regions of certain graphs, choose a different clustering type for t-SNE projections, download images, or adjust the number of rows displayed for tables. Clicking the question mark ? symbol next to graphs and metrics provides detailed descriptions.

The Cells and Library views both have a Gene Expression tab, which displays tables and plots depending on the experimental design. There are also additional tabs and metrics associated with VDJ-T, VDJ-B, and Feature Barcode analysis (Antibody, CRISPR).

The Experimental Design view has the same layout for all assay types. Click the question mark ? symbol to read descriptions for each section and metric.

Gene Expression tab

The web summary layout for Gene Expression libraries is described here.

Cells view

The Cells table contains the most important hero metrics for the sample. The t-SNE Projection section shows the data reduced to two dimensions, colored by UMI count or clustering (Graph-based by default). It is a good starting point to explore structure in the data. The Top Features by Cluster table shows the results of a differential gene expression analysis among clusters (Graph-based clusters by default). Click the question mark ? to read full descriptions for each one.



Library view

The library view contains metrics for the full library (cells and background), although the estimated number of cells is also reported here. The Cell Statistics table displays the most important results of the experiment. Additional metrics are displayed below the hero metrics in the Sequencing Metrics, Mapping Metrics, and Metrics per Physical Library tables. Click the question mark ? to read full descriptions for each one.



The GEX Barcode Rank Plot for the gene expression data enables one to assess library quality. Ideally there is a steep drop-off separating high UMI count cells from low UMI count background noise.

The Sequencing Saturation plot allows the user to assess the relative trade-offs of sequencing deeper or shallower. As sequencing saturation increases, the total number of molecules detected in the library increases, but with diminishing returns as saturation is approached.



The Median Genes per Cell plot allows the user to assess the relative trade-offs of sequencing deeper or shallower. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.

VDJ-T and VDJ-B tab

The VDJ-T and VDJ-B tabs have metadata and metrics for the T cell and B cell libraries, respectively. This section displays screenshots for the VDJ-T tab, however, it is applicable to the VDJ-B tab as well.

Cell view

The T/B Cell Expression section contains metrics regarding T and B cell expression, and the V(D)J Annotation section contains metrics regarding V(D)J annotations.



A histogram for the top 10 clonotypes, and a list of their CDR3 sequences, frequencies, and proportion are also provided:



Library view

The library view contains metrics for the full library (cells and background), although the estimated number of cells is also reported here. Click the question mark ? to read full descriptions for each one. There are three main sections:



The V(D)J Barcode Rank Plot enables one to assess sample quality. Ideally there is a steep dropoff separating high UMI count cells from low UMI count background noise:



VDJ-T(G/D) tab

The cellranger multi pipeline allows users to analyze TCR libraries enriched for gamma (TRG) and delta (TRD) chains. If the cellranger multi run includes a gamma-delta enriched library, a new tab called VDJ-T(G/D) is created in the web_summary.html. The structure and contents of this tab are similar to the VDJ-T tab.

10x Genomics does not provide reagents or primers for TRG/D chain enrichment. Since this workflow is not fully supported, the Cell Ranger pipeline has not be extensively tested for TRG/D libraries, and the algorithm's performance cannot be guaranteed. An alert is displayed on the web_summary.html to indicate that the workflow is unsupported:



Feature Barcode tabs

Antibody and CRISPR web summary tabs have been described on the corresponding 3' Single Cell Gene Expression Feature Barcode section.

Experimental Design view

Experimental Design view shows the experimental design for the dataset:



The multi config CSV file is also included for troubleshooting convenience:



Visit the Summary Metrics page to understand the metrics_summary.csv output file. If you have any questions or feedback, please contact support@10xgenomics.com.

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