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Getting Started

Getting Started with Cell Ranger

Barcode Enabled Antigen Mapping (BEAM) is unsupported with GEM-X chemistry; therefore, Cell Ranger does not support BEAM/Antigen Capture libraries produced with this chemistry.
Starting with v8.0, support for Low Throughput (LT) libraries has been disabled in Cell Ranger. Please use v7.2 to analyze LT libraries.
  1. 1

    Introduction

    What is Cell Ranger?Supported librariesWhat is Feature Barcode?What is Fixed RNA Profiling?What is Cell Multiplexing?What is Antigen Capture (BEAM)?What is HT (High Throughput)?Experimental design for Immune Profiling
  2. 2

    Set up

    System requirementsDownloadInstallCloud Analysis
  3. 3

    Pipelines and inputs

    Choose a pipelineIdentify input filesCommand line arguments
  4. 4

    Review outputs

    Output file overview
  5. 5

    Other resources

    TutorialsGlossaryAdvancedPublic datasets