Supported Pipelines and Products

Legend

HT	High Throughput Learn more
Standard	Standard Kit
LT	Low Throughput Learn more

¹ At this time, reanalysis of aggregated count runs is not available in Cloud Analysis.

More on Supported Pipelines

• Cell Ranger count
  • Takes uploaded 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.
  • When feature barcode data is present, the pipeline first extracts and corrects the cell barcode and UMI from the feature library using the same methods as gene expression read processing. It then then matches the Feature Barcode read against the list of features declared in the Feature Barcode Reference.
  • Visit the Cell Ranger documentation to learn about Cell Ranger count parameters and outputs.
• Cell Ranger multi
  • This is the recommended pipeline when analyzing 3' Gene Expression data that was multiplexed with our CellPlex Multiplexing Solution or when analyzing V(D)J and 5' Gene Expression / Feature Barcode data from the same source sample.
  • Visit the Cell Ranger Single Cell Gene Expression documentation to learn about Cell Ranger multi for cell multiplexing analysis.
  • Visit the Cell Ranger Single Cell Immune Profiling documentation to learn about Cell Ranger multi for immune profiling analysis.
• Cell Ranger aggr
  • Aggregates outputs from multiple runs of Cell Ranger count or VDJ, recomputing the feature-barcode matrices and analysis on the combined data. This pipeline can be used to combine data from multiple samples into an experiment-wide feature-barcode matrix and analysis.
  • Visit the Cell Ranger documentation to learn about Cell Ranger aggr parameters and outputs.
• Cell Ranger V(D)J
  • 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.
  • Currently, the 10x Cloud Platform does not support Cell Ranger vdj in de novo mode (without a reference). This option may become available in a future release.
  • Visit the Cell Ranger documentation to learn about Cell Ranger V(D)J parameters and outputs.
• Cell Ranger reanalyze
  • Takes feature-barcode matrices produced by Cell Ranger count and reruns the dimensionality reduction, clustering, and gene expression algorithms using customizable parameter settings.
  • Visit the Cell Ranger documentation to learn about Cell Ranger reanalyze parameters and outputs.
• Cell Ranger ARC count
  • Takes uploaded 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, chromatin accessibility, and feature linkage analysis.
  • Visit the Cell Ranger ARC documentation to learn about Cell Ranger ARC count parameters and outputs.
• Cell Ranger ARC aggr
  • Aggregates outputs from multiple runs of Cell Ranger ARC count, recomputing the analysis on the combined data. This pipeline can be used to combine data from multiple samples into an experiment-wide matrix and analysis.
  • Visit the Cell Ranger ARC documentation to learn about Cell Ranger ARC aggr parameters and outputs.
• Cell Ranger ARC reanalyze
  • Takes matrices produced by Cell Ranger ARC count and reruns the dimensionality reduction, clustering, and other algorithms using customizable parameter settings.
  • Visit the Cell Ranger ARC documentation to learn about Cell Ranger ARC reanalyze parameters and outputs.