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10x Genomics
Chromium Single Cell Gene Expression

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 Barcode 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

Protein Aggregate Barcodes

Starting from Cell Ranger 6.1, a new antibody_analysis directory contains detailed information about detected protein aggregate barcodes in a CSV file named aggregate_barcodes.csv. The file shows antibody barcodes that were detected as aggregates, the number of UMI corrected reads, what fraction of reads are corrected for that particular barcode, and what fraction of the total reads are on that barcode.

$ head -5 antibody_analysis/aggregate_barcodes.csv
barcode,library_type,umi_corrected_reads,Fraction Corrected Reads,Fraction Total Reads
ATCGTAGCAGCGTATT-1,Antibody Capture,1965,0.016,0.002
CTACGGGGTTCTCGTC-1,Antibody Capture,1900,0.014,0.002
CTCCGATGTAGTAAGT-1,Antibody Capture,2968,0.018,0.002
CTCCGATGTTGATGTC-1,Antibody Capture,3691,0.02,0.003

Web Summary

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

Starting from Cell Ranger 6.1, on both count and multi web summaries, the histograms on UMI counts will be shown for features that were specified as Antibody Capture in the Feature Barcode reference file.

cellranger web summary