10x Genomics
Chromium Single Cell Immune Profiling
Cell Ranger7.1 (latest), printed on 12/18/2024
Understanding Cell Ranger multi Output
This page describes the cellranger multi output file structure, specifically for 5' Chromium Single Cell Gene Expression (GEX), V(D)J, Antibody Capture (cell surface protein), and 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/ subfolder contains the main pipeline outputs:
Contents of the outs/ folder
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TCR with gamma-delta chains
The cellranger multi pipeline allows users to analyze TCR libraries enriched for gamma (TRG) and delta (TRD) chains. However gamma-delta analysis is not a supported workflow and algorithm performance cannot be guaranteed. TRG/D outputs are located in the |
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:
| Name | Description |
|---|---|
count | Folder containing unfiltered results of 5' Single Cell Gene Expression analysis (cell-associated and background barcodes), described in the Raw Outputs section. |
vdj_b | Folder containing unfiltered V(D)J Immune Profiling analysis results for any B cells (cell-associated and background barcodes), described in the Raw Outputs section. |
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. |
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. |
per_sample_outs/: folder containing filtered data, i.e., only cell-associated barcodes in this sample. The contents of this folder are described here:
| 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. |
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. |
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. |
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. |