Cell Ranger is a software package designed to process single cell datasets generated by 10x Genomics Chromium instruments. Cell Ranger includes six primary pipelines to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more:

• cellranger multi is the recommended pipeline to analyze almost all 10x Genomics Chromium single cell datasets. It inputs FASTQ files from a combination of libraries generated from a single GEM Well. Similar to cellranger count (see below), cellranger multi performs alignment, filtering, barcode counting, and UMI counting. It uses the cell barcodes to generate feature-barcode matrices, determine clusters, perform gene expression analysis, and provide preliminary cell type annotations. It is the only available pipeline for analyzing 3'/5 Sample Multiplexing, Flex v1, Flex v2, and 5' Antigen Capture (BEAM) data.

• cellranger count takes FASTQ files and performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis. The cellranger count pipeline can take input from multiple sequencing runs on the same GEM Well. This pipeline can analyze Chromium 3′ Gene Expression assays (eg: 3’ v1, v2, v3, 5’ v1), but does not support newer data types (e.g., 3’/5’ Sample Multiplexing, Flex, or 5′ Antigen Capture). For these libraries, use cellranger multi instead.

• cellranger vdj takes FASTQ files for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser. As with cellranger count, this is an older pipeline and it is generally recommended to use cellranger multi instead.

• cellranger aggr aggregates outputs from multiple runs of cellranger count, cellranger vdj, or cellranger multi, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data. The aggr pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis.

• cellranger reanalyze takes feature-barcode matrices produced by cellranger count, cellranger multi, or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings.

• cellranger annotate takes the molecule_info.h5 and an optional .cloupe file produced by cellranger count, cellranger multi, or cellranger aggr to generate cell type annotations. This method assigns cell types by comparing each cell's gene expression profile to annotated reference datasets, providing a starting point for annotating your samples.

1. Run Cell Ranger on 10x Genomics Cloud Analysis

   Skip Cell Ranger download and installation and get started with 10x Genomics Cloud Analysis, our recommended method for running Cell Ranger pipelines for most new customers. Use your web browser to easily generate Cell Ranger outputs from your FASTQ files and aggregate outputs from multiple runs, free for every 10x Genomics sample. Sign up for a free account or view tutorials and learn more.

2. Install and run Cell Ranger on your own computing infrastructure

   Learn how to install and run Cell Ranger.