10x Genomics Support/Cell Ranger 7.2/Analysis/

Cell Ranger multi Outputs Overview

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 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/ subfolder contains the main pipeline outputs:


Important
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 outs/multi/vdj_t_gd and outs/per_sample_outs/mySample/vdj_t_gd folders. Output files in the vdj_t_gd folder are similar to those of vdj_t/b.
  • 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:
NameDescription
countFolder containing unfiltered results of 5' Single Cell Gene Expression analysis (cell-associated and background barcodes), described in the Raw Outputs section.
vdj_bFolder 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_tFolder 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_gdFolder 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:
NameDescription
web_summary.htmlRun summary metrics and charts in HTML format, described in the Web Summary page.
metrics_summary.csvRun summary metrics file in CSV format, described in the Metrics page.
countFolder 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_bFolder 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_tFolder 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_gdFolder 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_analysisFolder 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.
Cell Ranger multi web summary