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10x Genomics
Chromium Single Cell Immune Profiling

Different Ways of Running Cell Ranger

There are four primary ways to run Cell Ranger:

  1. 10x Genomics Cloud Analysis: a scalable platform for data management, analysis and collaboration to simplify and accelerate the interpretation of data generated from 10x Genomics assays (currently offered for U.S. customers only).
  2. Single Server: Cell Ranger can run directly on a dedicated server. This is the most straightforward approach and the easiest to troubleshoot.
  3. 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.
  4. 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.


Cell Ranger computing options for 5' Single Cell V(D)J Immune Profiling are identical to the computing options for 3' Single Cell Gene Expression. While the page below is hosted on 3' Single Cell solution's section, it is equally applicable to 5' Immune Profiling solution: