Cell Ranger provides a set of analysis pipelines that process 3' Chromium Single Cell Gene Expression, 5' Chromium Single Cell Immune Profiling, and Fixed RNA Profiling datasets to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

The input files required to run Cell Ranger depend on the specific pipeline being used. Here is a list of input files required by Cell Ranger:

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

• Reference transcriptome: A reference transcriptome is a collection of all known transcripts 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).

• V(D)J reference: If your analysis includes a 5' Single Cell V(D)J library, your cellranger vdj or cellranger multi analysis requires a VDJ reference as input. 10x Genomics provides downloadable pre-built V(D)J references that are based on T cell receptor (TRA, TRB) and B cell immunoglobin (IGH, IGL, IGK) gene annotations in Ensembl version 94 for the human and mouse references. If you run cellranger vdj in denovo mode, you do not need to specify a V(D)J reference.

• Probe set reference : The cellranger multi pipeline requires a probe set reference CSV as input for Fixed RNA Profiling datasets. The human and mouse reference files are available on the Downloads page and in the Cell Ranger tarball.

• multi config CSV: 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. A multi config CSV is not required for other Cell Ranger pipelines.

• Feature Reference CSV: A Feature Reference CSV file is only required when processing Feature Barcode data. It declares the molecule structure and unique Feature Barcode sequence of each feature present in your experiment.

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