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Cell Ranger Inputs

Cell Ranger Inputs

Cell Ranger provides a set of analysis pipelines designed to process 3' Chromium Single Cell Gene Expression, 5' Chromium Single Cell Immune Profiling, and Fixed RNA Profiling datasets.

The required input files for running Cell Ranger vary depending on the chosen pipeline. To select the appropriate pipeline for your needs, please refer to the Choosing a pipeline page.

This page details the necessary input files for three specific Cell Ranger pipelines.

  • FASTQ files: Required. The FASTQ format is a text-based file format that contains nucleotide sequence information along with quality scores for each sequenced nucleotide. Typically, FASTQ files are provided by your sequencing core. If not available, you must convert BCL files to FASTQ using one of the following pipelines: cellranger mkfastq, Illumina's BCL Convert, or Illumina's bcl2fastq.

  • Reference transcriptome: Required. A reference transcriptome is a collection of all known transcript sequences from a given organism. 10x Genomics provides downloadable pre-built references transcriptomes for human and mouse for your Cell Ranger run. The cellranger mkref pipeline also enables custom reference creation for non-human, non-mouse species with a reference genome sequence (FASTA file) and gene annotations (GTF file).

  • Libraries CSV: Optional. Only required for analyzing Feature Barcode libraries with cellranger count. The Libraries CSV file declares the input FASTQ data for the libraries that make up a Feature Barcode experiment.

  • Feature Reference CSV: Optional. Only required when processing Feature Barcode data. It indicates the unique Feature Barcode sequence and the location of each feature present in your experiment.

For assistance with setting up your command, please visit the cellranger count pipeline page.

  • FASTQ files: Required. Described in the count section.

  • Reference transcriptome: Required. Described in the count section.

  • V(D)J reference: Required. 10x Genomics provides downloadable pre-built V(D)J references that are based on T cell receptor (TRA, TRB) and B cell immunoglobulin (IGH, IGL, IGK) gene annotations in Ensembl version 94 for the human and mouse references. Not required when running cellranger vdj in denovo mode. The cellranger multi pipeline does not support denovo mode.

For assistance with setting up your command, please visit the cellranger vdj pipeline page.

  • FASTQ files: Required. Described in the count section.

  • Reference transcriptome: Required. Described in the count section.

  • V(D)J reference: Optional. Only required if your analysis includes a 5' Single Cell V(D)J library. Described in the vdj section.

  • multi config CSV: Required. A configuration file in CSV format that specifies all the parameters required to analyze Single Cell Gene Expression, V(D)J, Feature Barcode, and Fixed RNA Profiling libraries using the cellranger multi pipeline. The multi config CSV is required only for the cellranger multi pipeline and is not necessary for other Cell Ranger pipelines.

  • Feature Reference CSV: Optional. Only required if a Feature Barcode library is included in your analysis. Described in the count section.

  • Probe set reference : Optional. Only required for Fixed RNA Profiling datasets. The human and mouse reference CSV files are available on the Downloads page and in the Cell Ranger tarball.

For assistance with setting up your command, please visit the relevant page for your specific experiment: