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Antibody Outputs

Cell Ranger outputs certain files that are specific to the Antibody Capture analysis, besides the Gene Expression 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).

To visualize cells in 2-D space, secondary analysis dimensionality reduction outputs for Antibody Capture libraries are provided in the analysis/ directory. Log-transformed antibody counts are used to perform these analyses for Antibody Capture libraries. This is in contrast to the gene expression side of the feature-barcode matrix, where these projections are run on the PCA-reduced space from raw counts.

Below are some examples of the PCA, t-SNE, and UMAP output projection files.

Principal Components Analysis (PCA):

$head -5 analysis/pca/antibody_capture_10_components/projection.csv Barcode,PC-1,PC-2,PC-3,PC-4,PC-5,PC-6,PC-7,PC-8,PC-9,PC-10 AAACAAGCACCATACT-1,-5.574515404720648,4.1250677853049735,0.3343758325171491,-0.9529782537962408,-1.8811942105099764,-0.4217695409442901,-1.9900329330389255,-1.2255017468251315,-1.3980947791205285,-1.1176859809904909 AAACAAGCACGTAATG-1,-6.983452898884609,-1.9379476767294177,-0.042479446422044376,-1.264967360758824,4.167549425417305,0.12065395835962933,-0.707084060668425,-2.9769215409849656,0.9053984182888417,-0.061563257127632665 AAACAAGCATGCAATG-1,-4.430486543723384,3.7442086078976002,-0.9447490398187632,-1.9902233589725338,-0.6258151384415838,-1.3582451690099415,-0.107256076231657,-1.6254493516586832,-0.43820589495677176,2.3253990939137505 AAACAAGCATTTGGGA-1,-4.945904594634436,4.017097394368968,-0.16688953081917113,-0.5729444140584459,-1.8303228981840096,-0.7755095535305054,-1.4069565944426259,-0.7969252558721216,-0.0011689859429466765,0.39202448730849027  The t-distributed Stochastic Neighbor Embedding (t-SNE): $ 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


The Uniform Manifold Approximation and Projection (UMAP):