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10x Genomics
Chromium Single Cell ATAC

Cell Ranger ATAC Installation

Cell Ranger ATAC is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles most of its own required software dependencies, which are pre-compiled to run on a wide range of Linux distributions. See the System Requirements page for details.

For convenience, the reference data package required for Cell Ranger ATAC is provided as a separate download. Both the software file and the reference data package can be found on the downloads page.

Download and Install

Although Cell Ranger ATAC can be placed in any location, we use /opt in this example. Reference files can also be placed in any location, and it is often convenient to place them in the same directory as Cell Ranger ATAC.

Step 1 – Download the Cell Ranger ATAC file.

Step 2 – Unpack the Cell Ranger ATAC file.

$ cd /opt
$ tar -xzvf cellranger-atac-2.0.0.tar.gz

This unpacks Cell Ranger ATAC, its dependencies, and the cellranger-atac script into a new directory called cellranger-atac-2.0.0.

Step 3 – Download the reference data files.

Step 4 – Unpack the reference data files.

$ 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 ATAC.

Step 5 – Prepend the Cell Ranger ATAC directory to your $PATH. This will allow you to invoke the cellranger-atac command.

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

$ export PATH=/opt/cellranger-atac-2.0.0:$PATH

You may wish to 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. We will review the information to ensure that Cell Ranger ATAC will run smoothly once you have generated your own Chromium data. Assuming you have installed Cell Ranger ATAC as described above, run the following commands.

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

If you plan to run Cell Ranger ATAC on a cluster, please 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, please send the output files as attachments to the software team.

Verify Installation

To ensure that the cellranger-atac pipeline is installed correctly, use cellranger-atac testrun. This test can take up to 60 minutes on a sixteen-core workstation. Assuming you have installed Cell Ranger ATAC into /opt, the command to run the test would look like the following:

$ export PATH=/opt/cellranger-atac-2.0.0:$PATH
$ cellranger-atac testrun --id=tiny
cellranger-atac testrun 2.0.0
Copyright (c) 2018 10x Genomics, Inc.  All rights reserved.

Running Cell Ranger ATAC in test mode...

Martian Runtime - 4.0.5

Running preflight checks (please wait)...
2018-09-17 20:44:33 [runtime] (ready)           ID.tiny.SC_ATAC_COUNTER_CS.SC_ATAC_COUNTER._BASIC_SC_ATAC_COUNTER._ALIGNER.SETUP_CHUNKS
2018-09-17 20:44:33 [runtime] (run:local)       ID.tiny.SC_ATAC_COUNTER_CS.SC_ATAC_COUNTER._BASIC_SC_ATAC_COUNTER._ALIGNER.SETUP_CHUNKS.fork0.chnk0.main

Pipestance completed successfully!

Saving diagnostics to tiny/tiny.mri.tgz

Diganostics will be saved whether the test succeeds or fails. This tiny.mri.tgz file contains diagnostic information 10x Genomics can use to help resolve any problems. If the pipeline fails and you need troubleshooting assistance, you can send this file directly to us from the command line.

$ cellranger-atac 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 the software team. If the pipeline is successful, you will see output files created in the outs/ subdirectory.