Important
Barcode Enabled Antigen Mapping (BEAM) is unsupported with GEM-X chemistry; therefore, Cell Ranger does not support BEAM/Antigen Capture libraries produced with this chemistry.
This page describes the cellranger multi output file structure, specifically for Singleplex Universal 3' and 5' Gene Expression (GEX), V(D)J, Antibody Capture (cell surface protein), and Barcode Enabled Antigen Mapping (Antigen Capture) data. For video or self-directed tutorials on running cellranger multi, visit the multi tutorial page.
The main output folder name is the same as the run ID specified in your cellranger multi run (e.g. sample345 shown on the multi pipeline page). The outs folder contains the main pipeline outputs:
config.csv: a duplicate of the input config CSV file.vdj_reference: folder containing a copy of the input V(D)J reference.multi: folder containing raw outputs, i.e., the data for all barcodes (GEMs), including cells and background. The contents of this folder are described below.per_sample_outs: folder containing filtered data, i.e., only cell-associated barcodes in this sample. The contents of this folder are described below.
| Name | Description |
|---|---|
count | Folder containing unfiltered results of 3' and 5' Gene Expression analysis (cell-associated and background barcodes), described in the Raw Outputs section. |
vdj_b | Folder containing unfiltered 5' V(D)J analysis results for any B cells (cell-associated and background barcodes), described in the Raw Outputs section. This folder is only produced if a VDJ-B (BCR) library is included in the analysis. |
vdj_t | Folder containing unfiltered V(D)J Immune Profiling analysis results for any T cell (cell-associated and background barcodes) expressing alpha-beta chains, described in the Raw Outputs section. This folder is only produced if a VDJ-T (TCR) library is included in the analysis. |
vdj_t_gd | Folder containing unfiltered V(D)J Immune Profiling analysis results for any T cell (cell-associated and background barcodes) expressing gamma-delta chains, described in the Raw Outputs section. This folder is only produced if a TCR gamma-delta library is included in the analysis. |
| Name | Description |
|---|---|
web_summary.html | Run summary metrics and charts in HTML format, described in the Web Summary page. |
metrics_summary.csv | Run summary metrics file in CSV format, described in the Metrics page. |
count | Folder containing the results of any gene expression and Feature Barcode analysis, similar to cellranger count, described in the Filtered Outputs section. Contains the feature-barcode matrix that can be used to load the data onto third party tools for downstream analysis. |
vdj_b | Folder containing the results of V(D)J Immune Profiling analysis for any B cells, similar to cellranger vdj, described in the Filtered Outputs section. This folder is only produced if a VDJ-B (BCR) library is included in the analysis. |
vdj_t | Folder containing the results of V(D)J Immune Profiling analysis for any T cells expressing alpha-beta chains, similar to cellranger vdj, described in the Filtered Outputs section. This folder is only produced if a VDJ-T (TCR) library is included in the analysis. |
vdj_t_gd | Folder containing the results of V(D)J Immune Profiling analysis for any T cells expressing gamma-delta chains, similar to cellranger vdj, described in the Filtered Outputs section. This folder is only produced if a TCR gamma-delta library is included in the analysis. |
antigen_analysis | Folder containing the results of Antigen Capture analysis. Only present if T/BCR Antigen Capture library included in analysis. Includes two files antigen_specificity_scores.csv and per_barcode.csv, described in the Filtered Outputs section. |