10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger7.1, printed on 11/05/2024

Cell Ranger V(D)J Algorithms Overview

The cellranger vdj pipeline can be used to analyze sequencing data produced from Chromium Next GEM Single Cell 5′ V(D)J libraries. It takes FASTQ files from cellranger mkfastq or bcl2fastq for V(D)J libraries and performs sequence assembly and paired clonotype calling. The pipeline uses the Chromium Cell Barcodes (also called 10x Barcodes) and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a .vloupe file which can be loaded into Loupe V(D)J Browser. Visit the What is Cell Ranger page to learn more about Cell Ranger for Immune Profiling.

This page provides an overview of the cellranger vdj algorithm.

Algorithm overview

Assemble contigs

• Filter out reads with noisy barcodes and UMIs that may arise from PCR errors, sequencing errors, etc.
• Trim adaptors and primer sequences from 5' and 3' ends of the reads.
• Generate full-length transcripts (contigs) from each chain in all observed GEMs/barcodes.

Annotate contigs

• Annotate contigs with V(D)J segment labels and locate CDR3 regions that form the transcript.
• Filter contigs that are full-length and productive.

Call cells

• Identify barcodes/GEMs that contain T or B cells.

Generate clonotypes

• Group cell-associated barcodes into clonotypes and filter out some cells.