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Cellranger flex

CellRanger Flex

Data Type

Fixed RNA Profiling data can be analyzed using the CellRanger software suite provided by 10X Genomics.

Barcodes

When analyzing 10X data produced by Fixed RNA Profiling, the barcode used for each sample must be listed at the time of analysis. This information will be used to automatically populate a configuration CSV used by cellranger multi for analyzing this sample type.

Probe Sets

By default, the Chromium Probe Set v1.0.1 will be used for analysis. Custom probe sets are also supported by this analysis workflow. First upload the probe set CSV provided by 10X Genomics as a Pipeline Reference, selecting the type "CellRanger Probe Set (CSV)". Then select that uploaded probe set when analyzing the associated sequencing data.

Parameters:

  • Reference Genome: Select the appropriate reference genome (human or mouse)
  • Custom Probe Set: Optionally select a custom probe set to use for analysis
  • Samples: List the samples used for each barcode (BC001, BC002, etc.)
  • CellRanger Version: Specify the CellRanger software version to be used for analysis
Technical Details

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

Citations:

This pipeline supports viewing its output using the embedded Single-Cell Dashboard App directly on the output dataset's Overview page.