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Cell Ranger
Overview
Getting Started
Downloads & Installation
Cell Ranger Commands
Analysis
Inputs
Overview
Custom Reference (mkref)
FASTQs
Generating FASTQs (mkfastq)
Specifying FASTQs
FASTQs with Illumina software
Running Pipelines
Choosing a pipeline
Library types
GEX (count)
Antibody/CRISPR (count)
3' Cell Multiplexing (multi)
VDJ-T/B only (vdj)
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: v7.2.0 (Latest)
Click here for older versions
10x Genomics Support
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Cell Ranger
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Analysis
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Feature-Barcode Matrices from Cell Ranger Pipelines
Formats
MEX Format
HDF5 Format
On This Page
Formats