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10x Genomics
Chromium Single Cell Multiome ATAC + Gene Exp.

Cell Ranger ARC Installation

Cell Ranger ARC is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its required software dependencies, which are pre-compiled to run on a wide range of Linux distributions.

For convenience, the reference data package required for Cell Ranger ARC is provided as a separate download.

Download and Install

Step 1 – Download and unpack the cellranger-arc-2.0.1.tar.gz tar file in any location. In this example we use /opt.

$ cd /opt
[ download file from downloads page ]
$ tar -xzvf cellranger-arc-2.0.1.tar.gz

This unpacks Cell Ranger ARC, its dependencies, and the cellranger-arc script into a new directory called cellranger-arc-2.0.1.

Step 2 – Download and unpack any of the reference data files in a convenient location:

[ download file from downloads page ]
$ tar -xzvf refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz

This creates a new directory called refdata-cellranger-arc-GRCh38-2020-A-2.0.0 that contains a single reference (in this case, GRCh38). Each reference contains a set of pre-generated indices and other data required by Cell Ranger ARC.

Step 3 – Prepend the Cell Ranger ARC directory to your $PATH. This will allow you to invoke the cellranger-arc command.

If you unpacked both Cell Ranger ARC and the reference data into /opt, then you would run the following command:

$ export PATH=/opt/cellranger-arc-2.0.1:$PATH

You may add this command to your .bashrc for convenience.

Site Check Script

Next, run the bundled site check script and send the output to 10x Genomics. If requested, we will review the information to ensure that Cell Ranger ARC will run smoothly once you have generated your own Chromium data. Assuming you have installed Cell Ranger ARC as described above, please run the following commands after replacing the code in red with your email:

$ cellranger-arc sitecheck > sitecheck.txt
$ cellranger-arc upload [email protected] sitecheck.txt

If you plan to run Cell Ranger ARC on a cluster, run and send us the output twice, once on a submit host and once on a cluster node.

If your system does not have direct Internet connectivity, send the output files as attachments to [email protected].

Verify Installation

To ensure that the cellranger-arc pipeline is installed correctly, use cellranger-arc testrun. This test typically takes 10-20 min but can take up to 60 min on a sixteen-core workstation. Assuming that Cell Ranger ARC into /opt has been installed, the command to run the test would look like:

$ export PATH=/opt/cellranger-arc-2.0.1:$PATH
$ cellranger-arc testrun --id=tiny
 
Martian Runtime - v4.0.5
 
...
 
Pipestance completed successfully!
 
yyyy-mm-dd hh:mm:ss Shutting down.

This test should produce a folder named tiny, with the tiny.mri.tgz file, which contains diagnostic information and is generated irrespective of whether the pipeline succeeds or fails. If the pipeline fails and you need troubleshooting assistance, you can send this file directly to us from the command line. Replace the code in red with your email:

$ cellranger-arc upload [email protected] tiny/tiny.mri.tgz

If your system does not have direct Internet connectivity, you can also send the file as an attachment to [email protected].