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Cell Ranger
Miscellaneous
Cell Ranger
Overview
Getting Started
Supported Libraries
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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'/5' Sample Multiplexing (multi)
VDJ + GEX + Antibody/CRISPR/BEAM (multi)
Flex (multi)
Secondary Analysis
Aggregate Multiple Samples (aggr)
Cell Annotation (annotate)
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
Sample Multiplexing
VDJ-T/B
VDJ + GEX + BEAM
Flex
Tutorials
Algorithms
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Miscellaneous
Release Notes
Q&A
Glossary
Datasets
Loupe Browser
Version
v9.0 (Latest)
View source code
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
Human Readable List of Telemetry Metrics Collected by Cell Ranger Pipelines