Cell Ranger

Primary analysis

The primary analysis of raw sequencing files can be performed with several pipelines, notably the Cellranger pipeline developed by 10X Genomics. Cellranger uses predefined positions for adapter sequences, barcodes, and cDNA sequences, and employs the STAR alignment software to align reads to the reference genome. Reads that are not aligned or of poor quality are eliminated, and annotations are used to define exonic, intronic, and intergenic reads. The transcripts per cell quantification is based on counting Unique Molecular Identifiers (UMIs) for reads confidently aligned to the transcriptome and associated to a single cell barcode. This module is usually performed by the platform that owns the 10x Genomics Chromium system, such as UCAGenomiX.