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Cell Ranger


10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger Installation

Cell Ranger is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own 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 is provided as a separate download.

Download and install

Step 1 – Download and unpack the Cell Ranger file in any location. In this example we use /opt.

$ cd /opt
[ download file from downloads page ]
$ tar -xzvf cellranger-7.1.0.tar.gz

If you downloaded Cell Ranger in the .xz compression format, be sure to use the correct file extension tar.xz and tar flags to unpack:

$ cd /opt
[ download file from downloads page ]
$ tar -xvf cellranger-7.1.0.tar.xz

This unpacks Cell Ranger, its dependencies, and the cellranger script into a new directory called cellranger-7.1.0.

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

[ download file from downloads page ]
$ tar -xzvf refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0.tar.gz

This creates a new directory called refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0 that contains a single reference (in this case, GRCh38/Ensembl ). Each reference contains a set of pre-generated indices and other data required by Cell Ranger.

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

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

$ export PATH=/opt/cellranger-7.1.0:$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 will run smoothly once you have generated your own Chromium data. Assuming you have installed Cell Ranger as described above, run the following commands after replacing the code in red with your email:

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

If you plan to run Cell Ranger on a cluster, 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, you may send the output files as attachments to [email protected].

Verify installation

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

$ export PATH=/opt/cellranger-7.1.0:$PATH
$ cellranger testrun --id=tiny
Running Cell Ranger in test mode...
Martian Runtime - v4.0.0
Pipestance completed successfully!
yyyy-mm-dd hh:mm:ss Shutting down.
Saving pipestance info to "tiny/tiny.mri.tgz"

Whether the test pipestance succeeds or fails, you will see:

Saving pipestance info to "tiny/tiny.mri.tgz"

This tiny.mri.tgz file contains diagnostic information 10x Genomics can use to help resolve any problems, so it is generated whether the pipeline succeeds or fails. If the pipeline fails and you need troubleshooting assistance, you can send this file directly to 10x Genomics via the command line. Replace the code in red with your email:

$ cellranger 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].