Space Ranger2.0 (latest), printed on 12/22/2024
For convenient multi-sample analysis, the spaceranger aggr pipeline generates output files that contain all of the data from the individual input jobs, aggregated into single output files. The capture area suffix of each barcode is updated to prevent barcode collisions.
Each output file produced by spaceranger aggr follows the format described in the Understanding Output section of the documentation, but includes the union of all the relevant barcodes from each of the input jobs.
| spaceranger aggr does not perform a spot-calling step, it simply aggregates the spot calls from each input job into a final set of spot calls. Refer to the Tissue Detection section of the imaging algorithm for more details. |
A successful spaceranger aggr run should conclude with a message similar to this:
Outputs: - Aggregation metrics summary HTML: /opt/runs/AGG123/outs/web_summary.html - Aggregation metrics summary JSON: /opt/runs/AGG123/outs/summary.json - Secondary analysis output CSV: /opt/runs/AGG123/outs/analysis - Filtered feature-barcode matrices MEX: /opt/runs/AGG123/outs/filtered_feature_bc_matrix - Filtered feature-barcode matrices HDF5: /opt/runs/AGG123/outs/filtered_feature_bc_matrix.h5 - Copy of the input aggregation CSV: /opt/runs/AGG123/outs/aggregation.csv - Loupe Browser file: /opt/runs/AGG123/outs/cloupe.cloupe - Aggregated tissue positions list: /opt/runs/AGG123/outs/aggr_tissue_positions.csv - Spatial folder containing spatial images and scalefactors: /opt/runs/AGG123/outs/spatial Pipestance completed successfully!
Space Ranger v2.0 onwards there are two changes to the spaceranger aggr outputs: tissue_positions_list.csv was renamed to tissue_positions.csv and includes header row. If spaceranger aggr is run with samples from two different Space Ranger versions, the tissue_positions.csv will be reformatted to the new standard with header row. |
Upon completion, all the main pipeline outputs can be found in the outs/ subfolder which has the following structure from the example code:
outs ├── aggregation.csv ├── aggr_tissue_positions.csv ├── 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 ├── spatial │ ├── LV123 │ │ ├── scalefactors_json.json │ │ ├── tissue_hires_image.png │ │ └── tissue_lowres_image.png │ ├── LB456 │ │ ├── scalefactors_json.json │ │ ├── tissue_hires_image.png │ │ └── tissue_lowres_image.png │ └── LP789 │ ├── scalefactors_json.json │ ├── tissue_hires_image.png │ └── tissue_lowres_image.png ├── summary.json └── web_summary.html
The files are similar to the spaceranger count Gene Expression pipeline outputs. The aggr pipeline also outputs a copy of the input aggregation.csv.
Once spaceranger aggr has successfully completed
.cloupe file in Loupe Browser