
<SoftwareToggle
options={[
{
label: "Single Cell Gene Expression",
slug: "single-cell-gene-expression",
url: "/support/software/cell-ranger/7.2/antibody-capture-antigen-specificity-and-CRISPR-guide-capture-analysis/single-cell-gene-expression",
},
{
label: "Single Cell Immune Profiling",
slug: "single-cell-immune-profiling",
url: "/support/software/cell-ranger/7.2/antibody-capture-antigen-specificity-and-CRISPR-guide-capture-analysis/single-cell-immune-profiling",
},
{
label: "Fixed RNA Profiling",
slug: "fixed-rna-profiling",
url: "/support/software/cell-ranger/7.2/antibody-capture-antigen-specificity-and-CRISPR-guide-capture-analysis/fixed-rna-profiling",
},
]}
description={"Choose a product below to filter the page content to your needs:"}
active={"single-cell-gene-expression"}
/>

<LinkableSection id={"overview-a154cc"} title={"Overview"}>

Cell Ranger processes all Feature Barcode data through a counting pipeline called cellranger count that quantifies each feature in each cell. The pipeline outputs a unified **feature-barcode matrix** that contains gene expression counts alongside Feature Barcode counts for each cell barcode. The feature-barcode matrix replaces the gene-barcode matrix emitted by older versions of Cell Ranger.

The pipeline first extracts and corrects the cell barcode and UMI from the feature library using the same methods as gene expression read processing. It then matches the Feature Barcode read against the list of features declared in the [Feature Barcode Reference](/support/software/cell-ranger/7.2/analysis/running-pipelines/cr-feature-bc-analysis). The counts for each feature are available in the feature-barcode matrix output files and in the Loupe Browser output file.

</LinkableSection>

<LinkableSection id={"inputs-to-count-pipeline-9186a1"} title={"Inputs to Count pipeline"}>

To enable Feature Barcode analysis, cellranger count needs two new inputs:

- **Libraries CSV** is passed to cellranger count with the --libraries flag, and declares the FASTQ files and library type for each input dataset. In a typical Feature Barcode analysis there will be two input libraries: one for the normal single-cell gene expression reads, and one for the Feature Barcode reads. This argument replaces the --fastqs argument.
- **Feature Reference CSV** is passed to cellranger count with the --feature-ref flag and declares the set of Feature Barcode reagents in use in the experiment. For each unique Feature Barcode used, this file declares a feature name and identifier, the unique Feature Barcode sequence associated with this reagent, and a pattern indicating how to extract the Feature Barcode sequence from the read sequence. See Feature Barcode Reference for details on how to construct the feature reference.

</LinkableSection>

<LinkableSection id={"running-the-count-pipeline-9905da"} title={"Running the count pipeline"}>

<Image src={"https://cdn.10xgenomics.com/image/upload/v1650488473/FFPE-Visium_Comparison_April2021.jpg"} />

</LinkableSection>

<LinkableSection id={"feature-and-library-types-dbd155"} title={"Feature and library types"}>

When inputting Feature Barcode data to Cell Ranger via the Libraries CSV file, you must declare the library_type of each library. Specific values for library_type will enable additional downstream processing, specifically for Antibody Capture, Antigen Specificity, or CRISPR Guide Capture. The following table outlines the types of libraries that can be specified and what they mean for the downstream processing.

```
code block
```

<DocumentCallout>
<Text as={"span"}>Upgrading to Firmware 4.00 is required before running this assay. [Click here for the Chromium™ Controller Firmware Update Procedure](/support/instruments/chromium-controller/chromium-controller-firmware-update-procedure).</Text>
</DocumentCallout>

<Image src={"https://cdn.10xgenomics.com/image/upload/v1635972123/Technology%20Pages/10x_figures_Next-GEM-Technology-Page_Figure_2.png"} width={"770px"} />
<br />

| 10x Solution                                        | Gene Expression | Cell Surface Protein |
| --------------------------------------------------- | --------------- | -------------------- |
| Single Cell Gene Expression 3' v2                   | <Check />       | -                    |
| Single Cell Gene Expression 3' v3                   | <Check />       | <Check />            |
| Single Cell Gene Expression 3' v3.1                 | <Check />       | <Check />            |
| Single Cell Gene Expression 3' v3.1 (Dual Index)    | <Check />       | <Wrong />            |
| Single Cell Gene Expression 3' HT v3.1 (Dual Index) | <Check />       | <Check />            |
| Single Cell Gene Expression 3' LT v3.1 (Dual Index) | <Check />       | <Check />            |

</LinkableSection>


Antibody Capture, Antigen Specificity & CRISPR Guide Capture Analysis

A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.

Overview

Getting Started

Download Center

Cell Ranger Commands

Analysis

Tutorials

Algorithms

Advanced

Troubleshooting

Miscellaneous

Release Notes

Glossary

Datasets

Loupe Browser

Cell Ranger 7.2

Cell Ranger

Installation

Get Started with Cell Ranger

Convert BCL to FASTQ with Cell Ranger mkfastq

mkfastq

Cell Ranger mkfastq

Analyze Gene Expression and Feature Barcode data with Cell Ranger count

count

Cell Ranger count

aggr

Cell Ranger aggr

Rerun secondary analysis for a completed cellranger count or aggr run with different parameters

reanalyze

Cell Ranger reanalyze

Build a custom reference using Cell Ranger mkref

mkref

Cell Ranger mkref

Analyze cell multiplexing data with Cell Ranger multi

multi

Cell Ranger multi for 3' Cell Multiplexing

Analyze V(D)J and 5' GEX with Cell Ranger multi

multi for V(D)J

Cell Ranger multi for Immune Profiling

Analyze your GEX + VDJ + B cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-Ab

Analyze your GEX + VDJ + T cell Antigen Capture libraries with Cell Ranger multi

Cell Ranger multi for BEAM-T

Analyze V(D)J libraries with Cell Ranger vdj

Cell Ranger vdj

Capturing Neutrophils in 10x Single Cell Gene Expression Data

Capturing neutrophils

Capturing Neutrophils

Analyze scRNA-Seq Data From a Publication Using 10x Software

Data analysis

Example Data Analysis

Analysis and visualization of data in the tumor microenvironment application note using the Loupe and Loupe V(D)J Browsers

Characterize tumor cells

Tumor Microenvironment Data Analysis and Visualization

Understand pipeline telemetry data collection and learn how to disable it if needed

Cell Ranger Pipeline Telemetry

View all tutorials

Learn more about input files required to run Cell Ranger

Inputs

List of Inputs

Generating FASTQs

Specifying FASTQs

A CSV file used to indicate the input FASTQ files for libraries in a Feature Barcode experiment.

Libraries CSV

A CSV file used to indicate the molecule structure and unique Feature Barcode sequence of each feature present in the experiment.

Feature Reference CSV

A CSV files that specifies parameters required to run cellranger multi

Multi Config CSV

Custom Reference with mkref

Custom V(D)J Reference

Running Pipelines

Choosing a pipeline

GEX + Antibody/CRISPR (count)

VDJ-T/B only (vdj)

3'/5' Sample Multiplexing (multi)

VDJ + GEX + Antibody/CRISPR/BEAM (multi)

Flex (multi)

Aggregate Multiple Samples (aggr)

Cell Annotation (annotate)

Custom Analysis (reanalyze)

Learn more about the output files generated by Cell Ranger

Outputs

Web Summary

Metrics

Feature-Barcode Matrices

Molecule Info (H5)

Secondary Analysis

Results of aggr

Gene Expression

Antibody Capture

CRISPR Guide Capture

Sample Multiplexing

VDJ-T/B

VDJ + GEX + BEAM

Flex

What is Cell Ranger?

<Text as={'p'} size={'small'} weight={'medium'}>Cell Ranger v7.2 is the last version to support the analysis of LT (low throughput) libraries.</Text>

We provide resources from protocols, user guides, and free-to-use analysis tools

Algorithms overview

Advanced pipeline content for Cell Ranger.

Browse Q&As from the 10x Genomics support team.

View terms and definitions relevant to Single Cell products.

Access free public Chromium data from 10x Genomics.

A collection of introductions, tutorials, and blogs for data analysis beyond software.

Analysis Guides

Loupe Browser is a desktop application that allows you to interactively visualize data.

Other Resources