When performing a combined analysis of single-cell 5' transcriptome and V(D)J data, it is common to encounter situations where the number of cells differs significantly. Typically, two scenarios are observed:

1. Discrepancy in TCR analysis: In this case, the number of V(D)J cells is much smaller than the number of gene expression (GEX) cells. This discrepancy arises from the low expression levels of TCR genes, which may result in incomplete splicing and the loss of some genuine TCR genes, leading to false negative results.

2. Discrepancy in BCR analysis: In this scenario, the number of V(D)J cells is much higher than the number of GEX cells. This is often observed in BCR analysis, where the expression of BCR genes, particularly in plasma cells, is high. Consequently, there may be more background mRNA, leading to the calculation of empty droplets and resulting in false positive results.

To address these challenges, performing a joint analysis of V(D)J results and 5' transcriptome data is recommended. This integration enhances the accuracy of the analysis outcomes by incorporating information from both datasets.