Significant differences in cell counts between single-cell 5’ transcriptome and V(D)J joint analysis generally occur in two situations. One is when the V(D)J cell count is much lower than the GEX cell count, commonly seen with TCRs due to their often low expression levels, sometimes failing to capture the full-length gene, resulting in false negatives. The other is when the VDJ cell count is much higher than the GEX cell count, typically seen with BCRs due to their often high expression levels, particularly in the presence of plasma cells, where a large amount of background mRNA may cause empty droplets to be counted, leading to false positives. Therefore, combining VDJ results with 5' transcriptome data for joint analysis improves the accuracy of the results.