For convenient multi-sample analysis, the cellranger aggr pipeline generates output files that contain all of the data from the individual input jobs, aggregated into single output files. The GEM well suffix of each barcode is updated to prevent barcode collisions, as described below.
Each output file produced by
cellranger aggr follows the format described in the Understanding Outputs section of the documentation, but includes the union of all the relevant barcodes from each input job. For example, samples processed individually using
cellranger count and then aggregated using
aggr would generate final outputs similar to the count pipeline.
A successful cellranger aggr run should conclude with a message similar to this:
Outputs: - Aggregation metrics summary HTML: /home/jdoe/runs/AGG123/outs/web_summary.html - Copy of the input aggregation CSV: /home/jdoe/runs/AGG123/outs/aggregation.csv - Aggregation metrics summary JSON: /home/jdoe/runs/AGG123/outs/summary.json - Secondary analysis output CSV: /home/jdoe/runs/AGG123/outs/analysis - Filtered feature-barcode matrices MEX: /home/jdoe/runs/AGG123/outs/filtered_feature_bc_matrix - Filtered feature-barcode matrices HDF5: /home/jdoe/runs/AGG123/outs/filtered_feature_bc_matrix.h5 - Loupe Browser file: /home/jdoe/runs/AGG123/outs/cloupe.cloupe Pipestance completed successfully!
cellranger aggr has successfully completed, the outputs can be found in the outs/ sub-directory. The directory structure is shown here:
outs ├── aggregation.csv ├── count │ ├── analysis │ │ ├── clustering │ │ ├── diffexp │ │ ├── pca │ │ ├── tsne │ │ └── umap │ ├── cloupe.cloupe │ ├── filtered_feature_bc_matrix │ │ ├── barcodes.tsv.gz │ │ ├── features.tsv.gz │ │ └── matrix.mtx.gz │ ├── filtered_feature_bc_matrix.h5 │ └── summary.json └── web_summary.html
These files are similar to the
cellranger count Gene Expression pipeline outputs. In addition, the
aggr pipeline also outputs
aggregation.csv, a copy of the input aggregation CSV. The resulting web summary HTML file can be viewed in any supported web browser, and the .cloupe file can be opened in Loupe Browser.
If chemistry batch correction was specified (
batch column in input aggregation CSV file), the
web_summary.html files will contain batch effect scores before and after chemistry correction. Batch effect scores indicate whether there is a batch effect (greater than one) or no batch effect (closer to one) (read more on the gene expression algorithm page).
For more information on summary metrics, refer to the
cellranger aggr section of the Summary Metrics page. For
aggr datasets with 100k+ cells, Loupe Browser 6.0 and later is recommended for optimal performance.
cellranger aggr run includes cell surface protein/Antibody Capture libraries, an additional folder called
antibody_analysis is created. The contents of this folder are described on the Antibody Outputs page.
cellranger aggr run includes CRISPR Guide Capture libraries, an additional folder called crispr_analysis is created. The contents of this folder are described on the CRISPR outputs page.
For aggregating data generated using the 5' Chromium Next GEM Single Cell Immune Profiling solution, visit the 5' cellranger aggr page.