The reference genome used for single-cell V(D)J analysis cannot be shared with the reference genome used for single-cell RNA-seq. Although both reference genomes are specific to the same species, they are significantly different. Their focus and application scenarios vary in data analysis and processing.


The single-cell immune repertoire analysis primarily revolves around V(D)J recombination and clonotype identification of immune receptors, aiming to understand diversity, clonal expansion, and immune responses. Therefore, constructing a reference genome for single-cell immune repertoire requires special attention to the annotation and database of immune receptor-related genes, such as V, D, and J genes.


On the other hand, single-cell transcriptome studies focus on gene expression across the entire genome to unveil transcriptional signatures across different cell types and states. Consequently, when constructing a reference genome for single-cell transcriptomes, comprehensive genome-wide gene annotations and databases need to be considered.


Thus, due to the distinct foci and requirements of these analyses, separate reference genomes are necessary for single-cell V(D)J analysis and single-cell transcriptome analysis.