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Cell Ranger 7.2
Miscellaneous
Cell Ranger 7.2
Overview
Getting Started
Download Center
Cell Ranger Commands
Analysis
Inputs
Overview
Custom Reference with mkref
Custom V(D)J Reference
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
Inputs
Overview
Custom Reference with mkref
Custom V(D)J Reference
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
Algorithms
Advanced
Troubleshooting
Miscellaneous
Release Notes
Q&A
Glossary
Datasets
Loupe Browser
Version
v7.2
Click here for older versions
Miscellaneous
Converting 10x Genomics BAM Files to FASTQ
10x Genomics Citations
Mitigating Index Hopped Reads In Silico
Recommendation on Including Introns for Gene Expression Analysis
Data Transfers to 10x Genomics