10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger3.1, printed on 11/05/2024

Getting Started with Cell Ranger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

This getting started guide is a series of short tutorials designed to help you install and run the Cell Ranger pipelines on your system. It does not comprehensively cover all of the options and analysis cases Cell Ranger can handle, but provides a starting point and tips for further analysis.

Objectives

• Install the Cell Ranger Pipeline
• Check the system to see if it meets the system requirements
• Use cellranger upload to send data to 10X Genomics support
• Know where to get help
• Run cellranger mkfastq to generate FASTQ files using test data
• Run cellranger count using a public data set
• Run cellranger aggr to combine two data sets
• Run cellranger reanalyze to adjust clustering parameters

Tutorials

• Installing Cell Ranger
• Running cellranger mkfastq
• Running cellranger count
• Running cellranger aggr
• Running cellranger reanalyze