Question: How does Cell Ranger correct for amplification bias?
Answer: Each transcript captured in the Single Cell Gene Expression and V(D)J assay is labeled with a 10-12 bp Unique Molecular Identifier (UMI) in addition to a 16 bp cell barcode. After sequencing, the UMI is used to distinguish sequenced reads that originate from unique mRNA molecules vs PCR duplicates.
Multiple reads that match the same 10x barcode, UMI, and gene are collapsed to a single UMI count in the feature-barcode matrix.
For more information on UMI counting, please see: Gene Expression Algorithms Overview; Cell Ranger V(D)J Algorithms Overview.
Products: Single Cell Gene Expression, Single Cell Immune Profiling