10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.1, printed on 11/05/2024

Feature Barcoding Only Analysis

To reduce sequencing and library preparation costs, Feature Barcoding Only mode can be used. In Cell Ranger 3.1, cellranger countcan run using only Feature Barcoding libraries like an Antibody Capture library without sequencing the Gene Expression library.

To use cellranger in Feature Barcoding Only mode, follow instructions for Feature Barcoding Analysis, and omit Gene Expression entries from the Libraries CSV file. Results from Feature Barcoding Only analysis can be used with cellranger aggr, with the requirement that all aggregated runs must share a common feature reference.

Cell Ranger performs the normal Feature Barcoding quantification analysis in Feature Barcoding Only mode, but uses a simplified version of the cell calling algorithm. The EmptyDrops step that refines cell calls in not performed. See the Cell Calling algorithm documentation for details.

Run Summary

A web_summary.html file summarizing the run is produced as usual. Metrics for Antibody libraries appear under the Antibody Sequencing and Antibody Application sections. The Sequencing and Mapping sections, which display metrics from Gene Expression libraries, do not appear.

Analysis Results

Shown below are results for a single sample with Gene Expression and antibody Feature Barcoding libraries. On the left, both libraries are processed together, and the barcode-rank plot displays Gene Expression counts. On the right, only the Feature Barcoding library is supplied to cellranger count, and the barcode rank plot displays the antibody counts.

Observe that a similar number of cells were called in each cellranger run, but the shape of barcode-rank plot differs due to differences in the background levels of the Gene Expression and Antibody libraries.

Gene Expression + Feature Barcoding

Feature Barcoding Only

Effect of Antibody Panel

Feature Barcoding Only analysis only detects cells that are labelled by the Feature Barcoding reagents in use. Cell types not well-stained by the panel have low total UMI counts and may not be called by the cell-calling algorithm. The table below illustrates this effect by comparing the number of cell detected in the gene expression library and antibody capture library derived from the same cells. As the number of antibodies in the panel increases, the number of cells detected in the Feature Barcoding Only analysis approaches the number detected in the gene expression analysis. Below are results for a series of TotalSeq-B antibody panels applied to human PBMCs.