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# Output File Structure

This page describes the cellranger multi output file structure, specifically for 5' Chromium Single Cell Gene Expression (GEX) and V(D)J data. Refer to the multi pipeline page to learn about running cellranger multi.

The output folder name is the same as the run ID you specified (e.g. sample345 used on the Running multi page). The subfolder named outs/ contains the main pipeline outputs:

## Contents of the outs/ folder

• 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
count Folder containing unfiltered results of 5' single cell gene expression analysis (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 cells (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.

• 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, similar to cellranger vdj, described in the Filtered Outputs section.