Cell Ranger6.1, printed on 11/14/2024
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).
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
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
Summary metrics for the antibody counts will be displayed in the Summary view of the count web summary under Antibody Sequencing and Antibody Application, and in the Sample and Library views of the multi web summary under the Antibody tabs.
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.
Any specific antibody analysis steps are described in the Antibody Algorithms section.