Cell Ranger 1.0, printed on 03/23/2019
Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. There are two pipelines:
cellranger demux wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files.
cellranger run takes FASTQ files from cellranger demux and performs alignment, de-duplication and filtering, and uses the Chromium cellular barcodes to generate gene-cell matrices and perform clustering and gene expression analysis.
These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, and HTML formats that are augmented with cellular information.