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10x single cell sequencing cellranger

10X Single Cell Sequencing (cellranger)

Data Type

Single-cell sequencing data produced by the 10X platform can be analyzed using the CellRanger software suite produced by that company.

The CellRanger software suite can be run in many different ways, to account for all of the different ways that data can be collected from single cells.

Analysis options include:

5' Cell Multiplexing: Analysis of data produced by the 5' Cell Multiplexing platform is supported using the approach shown here. Use the CellRanger Hashtagging workflow to analyze this data.

Note: If your dataset has one set of reads which contains both the 5' Cell Multiplexing tags as well as feature barcode data, those files should be marked as Multiplexing Capture in the feature_types column of the samplesheet.csv. If a Feature Reference CSV is provided to the analysis, then those reads will be processed as feature barcode data after demultiplexing.

Fixed RNA Profiling + Feature Barcodes: If your dataset contains both fixed RNA profiling data and feature barcode data, you can use the CellRanger Multi Analysis workflow to analyze it. Make sure to select the "Fixed RNA Profiling" checkbox in the workflow options and enter the appropriate probe barcode information.

Reference Genomes:

  • Human reference (GRCh38) - 2024-A (and legacy 2020-A)
  • Mouse reference (GRCm39) - 2024-A (and legacy 2020-A)
  • Human (GRCh38) and mouse (GRCm39) reference - 2024-A (and legacy 2020-A)
  • Human V(D)J reference (GRCh38) - 7.1.0 (and legacy 7.0.0)
  • Mouse V(D)J reference (GRCm38) - 7.0.0
More Details

Workflow Repository: github.com/FredHutch/nf-cellranger-tools

Citations: