10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.1, printed on 11/14/2024

Antibody Outputs

Starting from Cell Ranger 3.0, all Feature Barcode counts, including Antibody Capture counts, simply become new features in addition to the standard per-gene features, and are output alongside gene counts in the feature-barcode matrix. For every row in the Feature Barcoding Reference CSV file where feature_type is specified as Antibody Capture, there will be a corresponding row in the feature-barcode matrix. That row will get its title from the id field in the Feature Reference file for that feature, and the counts can be visualized via Loupe Browser by searching for the human-readable name from the name field of the Feature Reference file (for antibody applications, the id and name fields can typically be the same as long as the id is unique).

We run t-distributed Stochastic Neighbor Embedding (t-SNE) on raw antibody counts (i.e., without prior PCA) to visualize cells in a 2-D space. This is in contrast to the gene-barcode side of the matrix, where t-SNE is run on the PCA-reduced space. For more details, see the "t-SNE" in Antibody Algorithms section.

$ head -5 analysis/tsne/antibody_capture_2_components/projection.csv
Barcode,TSNE-1,TSNE-2
AAACCCAAGTGGTCAG-1,-29.97926190939189,-3.5125258285933603
AAAGGTATCAACTACG-1,20.762905594110116,-6.946344013493825
AAAGTCCAGCGTGTCC-1,11.156075443007484,-5.489821984514518
AACACACTCAAGAGTA-1,-26.08126312702518,-5.167458628104057

Summary metrics for the antibody counts will be displayed on web summary under Antibody Sequencing and Antibody Application tabs. Any specific antibody analysis steps are described in the Antibody Algorithms section.