10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger5.0, printed on 11/05/2024

Cell Ranger V(D)J Algorithms Overview

The figure above shows 10x V(D)J read-pairs aligned to an assembled contig, illustrating the structure of the read data. One to several UMIs are captured for each V(D)J chain. A round of enrichment PCR targeting the 5′ end to the C-region, followed by enzymatic fragmentation results in a pool of molecules originating from the same transcript. The molecules carry the same 10x barcode and UMI sequences, but with different insert lengths, resulting in different R2 start points. The diversity of R2 start points gives complete coverage of the targeted portion of each transcript, which is typically ~650bp.

• Assembly Algorithm - Assembles read-pairs into one contig for each transcript sequence.
• VDJ Cell Calling Algorithm - Identifies barcodes that contain T or B cells.
• Annotation Algorithm - Annotates contigs with V(D)J segment labels and locates CDR3 regions.
• Clonotype Grouping - Groups cells into clonotypes and in doing so filters out some cells.
• iNKT and MAIT cell Algorithms - Annotates T cells as potential iNKT or MAIT cells based on V(D)J data.
• Glossary of Terms - Definitions of important terms.