Cell Ranger Reference Package build guide

This guide explains how to manually install 10x Genomics Cell Ranger 9.0.1 on a Linux-based virtual machine or server.

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General Information

This guide consists of step-by-step instructions to install Cell Ranger 9.0.1 on a Linux VM, and 2 scripts to build the reference data for GRCh38 and mm10 reference packages. The scripts you can find in build_grch38_reference.sh and build_mm10_reference.sh. (These are exactly the same scripts copied from 10X official website with additional logging).

Prerequisites

• A 64-bit Linux VM (e.g., Ubuntu 20.04 or later)
• sudo access
• Internet connection
• Approximately 6 GB of free disk space

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Step 1: Download Cell Ranger

Access the link for Cell Ranger

Navigate to the download section and copy wget command for Cell Ranger 9.0.1 (it should look like this):

wget -O cellranger-9.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-exp/cellranger-9.0.1.tar.gz?Expires=1748429361&Key-Pair-Id=SomeTokenBLuhBluh"

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Step 2: Install Cell Ranger to /opt

# Move the archive to /opt
sudo mv cellranger-9.0.1.tar.gz /opt/

# Extract the archive in /opt
sudo tar -xzf /opt/cellranger-9.0.1.tar.gz -C /opt

# (Optional) Remove the archive to free up space
sudo rm /opt/cellranger-9.0.1.tar.gz

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Step 3: Create a Symlink to cellranger

This allows you to run cellranger from anywhere:

sudo ln -s /opt/cellranger-9.0.1/cellranger /usr/local/bin/cellranger

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Step 4: Verify the Installation

which cellranger
cellranger --version

Expected output:

/usr/local/bin/cellranger
cellranger 9.0.1

Step 5: Building the Reference Data

After installing Cell Ranger, you can build the reference data for GRCh38 or mm10 by exectuing the scripts:

./build_grch38_reference.sh

Output: will be placed in {reference_name}_build directory such as GRCh38-2020-A_build. To see the gene list access gene_allowlist file.

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Notes

• Cell Ranger is only supported on Linux (x86_64 architecture).
• This setup is ideal for personal servers, academic compute nodes, or cloud-based VMs.
• See the official reference download page:
  https://www.10xgenomics.com/support/software/cell-ranger/downloads