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Cell Ranger
Analysis
Feature-Barcode Matrices from Cell Ranger Pipelines
Cell Ranger
Overview
Getting Started
Supported Libraries
Download Center
Cloud Analysis
Cell Ranger Commands
Analysis
Inputs
List of Inputs
Generating FASTQs
Specifying FASTQs
Libraries CSV
Feature Reference CSV
Multi Config CSV
Custom Reference with mkref
Custom V(D)J Reference
Running Pipelines
Choosing a pipeline
Library types
GEX + Antibody/CRISPR (count)
VDJ-T/B only (vdj)
3' Cell Multiplexing (multi)
VDJ + GEX + FB/BEAM (multi)
Fixed RNA Profiling (multi)
Secondary Analysis
Aggregate Multiple Samples (aggr)
Custom Analysis (reanalyze)
Outputs
Overview
Web Summary
Metrics
Feature-Barcode Matrices
BAM
Molecule Info (H5)
Secondary Analysis
Results of aggr
Library types
Gene Expression
Antibody Capture
CRISPR Guide Capture
Cell Multiplexing
VDJ-T/B
VDJ + GEX + BEAM
Fixed RNA Profiling
Tutorials
Algorithms
Advanced
Troubleshooting
Miscellaneous
Release Notes
Q&A
Glossary
Datasets
Loupe Browser
Version
v8.0 (Latest)
Click here for older versions
Feature-Barcode Matrices from Cell Ranger Pipelines
Formats
MEX Format
HDF5 Format
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