Why is the number of V(D)J-detected cells lower than the number of T/B cells identified from transcriptome data (when T/B cell origin is confirmed)?

Answer:
This is most commonly caused by sample quality issues and differences in detection principles between transcriptome and V(D)J analysis.

1. Different identification logic

• Transcriptome identifies T/B cells based on marker gene expression 
• V(D)J analysis requires productive V(D)J transcripts + sufficient UMI support + filtering of ambient RNA

Therefore, transcriptome analysis generally detects more T/B cells.

2. Productive V(D)J determination is stringent:

• Requires read alignment, assembly, filtering, and annotation. Any failure in these steps may result in a transcript being classified as non-productive

3. Low expression or RNA degradation:

• V(D)J transcripts are relatively low-abundance 
• Poor sample quality (low viability / RNA degradation) further reduces successful capture and assembly 

Conclusion: If transcriptome analysis shows many T/B cells but V(D)J recovery is low—especially with a low proportion of Cells With Productive V-J Spanning Pair—this strongly indicates sample quality issues.

Recommendation: Use fresh, high-quality samples, especially for immune repertoire analysis where full-length V(D)J recovery is required.