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To set up and run Cell Ranger ATAC on Linux, please follow the steps below, or skip download and installation and get started with 10x Cloud Analysis:

Cell Ranger ATAC 2.2.0 (Apr 30, 2025)

Chromium Single Cell Software Suite
Self-contained, relocatable tar file. Does not require centralized installation.
Contains binaries pre-compiled for CentOS/RedHat 7.0 and Ubuntu 18.04.
Runs on Linux systems that meets the minimum compute requirements.

tar.gz compression

Download for Linux 64-bit (tar.gz)

File size: 661 MB

md5sum: c616198bd9aaca393f99c71e07ae46b6

curl

wget


curl -o cellranger-atac-2.2.0.tar.gz "https://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-2.2.0.tar.gz?Expires=1748200538&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=Qy1qajMQGFSlkD4DnG4xy~uxm5UPW6Azs8ImlOqbgicxFuhAQKcS6zgKXtARxQz5gAW59jWv~RfCHc77OGlKby9rPFHFjSecmq-u9hGDyPj1Usa6iWXV~Drx8qs7yB206B7drHGIDu9I7BwYT4RVxXO2AcCV7~jkHmSY4i~WyLLVeW-iowmNT19ugxHiwpw7eMs8AkZwVN92YFyAdgmNTxebU138D-zeeB9Gm1~FUGN5AYUf49ivJbsfMU2ObTbQSbUDB6St1Acz4KttzjjzjCg~7jUlRhowtBqWcTATFhCIPBkbcBlPmBN856qASHandb5SdaGlEoV1IL94v4dxBA__"

Download is unavailable on mobile devices.

Cell Ranger ATAC 2.2.0 highlights

The 20,000 total cell limit has been removed from cellranger-atac pipelines, enabling the analysis of large datasets
Strand information is now included in the fragments.tsv file for easier downstream analysis
The --nosecondary parameter is now enabled for count and aggr pipelines
Minor performance improvements

Previous versions

Release notes

References

View steps to build references

Human reference (GRCh38) - 2024-A
- Human reference (GRCh38) dataset required for Cell Ranger ATAC.
Download Human Reference
File size: 14 GB
md5sum: 57a41ecf38b1ec2ef66b3d345ad05839
curl
wget
```
curl -O "https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2024-A.tar.gz"
```
Mouse reference (GRCm39) - 2024-A
- Mouse reference (GRCm39) required for Cell Ranger ATAC.
Download Mouse Reference
File size: 13 GB
md5sum: 25c52a830d5f749558f84e1400c71486
curl
wget
```
curl -O "https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCm39-2024-A.tar.gz"
```
Human and Mouse reference (GRCh38 and GRCm39) - 2024-A
- Human and Mouse reference (GRCh38 and GRCm39) required for Cell Ranger ATAC.
Download Human and Mouse Reference
File size: 29 GB
md5sum: 2c0637691c9a22f99eef2ae55438faab
curl
wget
```
curl -O "https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-and-GRCm39-2024-A.tar.gz"
```

Download is unavailable on mobile devices.

Compute Platforms

Compute platforms

View options for compute platforms

System requirements

View the minimum requirements to run Cell Ranger ATAC pipelines

Installation

Cell Ranger ATAC installation

View instructions on how to install Cell Ranger ATAC