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10x Genomics
Chromium Single Cell Gene Expression

Different Ways of Running Cell Ranger

Table of Contents

There are three primary ways to run Cell Ranger:

  1. Single Server: Cell Ranger can run directly on a dedicated server. This is the most straightforward approach and the easiest to troubleshoot.
  2. Job Submission Mode: Cell Ranger can run using a single node on the cluster. Less cluster coordination is required since all work is done on the same node. This method works well even with job schedulers that are not officially supported.
  3. Cluster Mode: Cell Ranger can run using multiple nodes on the cluster. This method provides high performance, but is difficult to troubleshoot since cluster setup varies among institutions.


Single Server

Local Mode

The majority of the information on this website uses the single server approach. Follow the instructions below to analyze a 10x library:

  1. Generating FASTQs
  2. Specifying Input FASTQs
  3. Single-Library Analysis


Job Submission Mode

Cell Ranger can be run in job submission mode, by treating a single node from the cluster like a local server. This leverages existing institutional hardware for pipeline analysis.

Hybrid Mode

This mode of operation is what most people have in mind when it comes to working with clusters; a large computational job is submitted to the cluster, and there is one Job ID to track during job execution. To learn more, please go to the job submission mode page.


Cluster Mode

Cell Ranger can be run in cluster mode, using SGE or LSF to run the stages on multiple nodes via batch scheduling. This allows highly parallelizable stages to utilize hundreds or thousands of cores concurrently, dramatically reducing time to solution.

Cluster Mode

Instead of submitting one job to the cluster, Cell Ranger creates hundreds and potentially thousands of small stage jobs. Each of these stage jobs need to be queued, launched, and tracked by the pipeline framework. The necessary coordination between Cell Ranger and the cluster makes this approach harder to set up and troubleshoot, since every cluster configuration is different. To learn more, please go to the cluster mode page.