Interference of B-Cell and T-Cell Receptor Genes in Single-Cell RNA Sequencing Data

B and T cells play central roles in immune responses and, as such, are integral in many diseases, such as autoimmunity. Characterizing these cells, their subsets, and exploring their transcriptomes to understand the underlying biology, can be achieved using single-cell RNA sequencing (scRNA-seq). While some studies report removing the transcripts encoding the variable regions of the B- and T-cell antigen receptors prior to downstream analyses, a systematic analysis of the effects of retaining versus removing these genes has been lacking. We investigated the effects these transcripts in B and T cells impose on supervised clustering and downstream analyses of scRNA-seq data.