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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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Advanced
Cell Ranger's Web Summary Antibody Barcode Rank Plot
Cell Ranger's Web Summary Barcode Rank Plot
Cluster Mode
Cell Ranger Command Line Arguments (Manual Page)
Job Submission Mode
The Cell Ranger User Interface
Cell Ranger Multi Config CSV (Manual Page)
Pipestance Structure