Cell Ranger

What is Cell Ranger?

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.

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Analysis

Inputs

Learn more about input files required to run Cell Ranger

Running Pipelines

Learn more about how to run Cell Ranger

Outputs

Learn more about the output files generated by Cell Ranger

Tutorials

Get Started with Cell Ranger

Cell Ranger installation

Cell Ranger mkfastq

Convert BCL to FASTQ with Cell Ranger mkfastq

Cell Ranger count

Analyze Gene Expression and Feature Barcode data with Cell Ranger count

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Algorithms overview

Overview of algorithms.

Advanced

Advanced pipeline content for Cell Ranger.

Release Notes

View the latest updates to Cell Ranger.

Q&A

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

Glossary

View terms and definitions relevant to Single Cell products.

Datasets

Access free public Chromium data from 10x Genomics.

Analysis Guides

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

Loupe Browser

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