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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger7.1, printed on 11/21/2024

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 available for customers in the U.S. and Canada 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.

Recommendations and requirements, in order of computational speed (left to right):
Cloud Analysis Cluster Mode Job Submission Mode Single Server
Recommended for Default option for users in supported countries Organizations using an HPC with SGE or LSF for job scheduling Organizations using an HPC Users without access to an HPC, if Cloud Analysis is not an option
Compute details Splits each analysis across multiple compute nodes to decrease run time Splits each analysis across multiple compute nodes to decrease run time Runs each analysis on a single compute node Runs each analysis directly on a dedicated server
Requirements Any laptop or desktop computer HPC with SGE or LSF for job scheduling HPC with most job schedulers Linux computer with minimum 8 cores & 64 GB RAM

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 the 3' Single Cell solution's section, it is equally applicable to the 5' Immune Profiling solution:

  • Computing Options - 3' Gene Expression