Can 5’ scRNA-seq libraries and V(D)J libraries be sequenced together? What pooling ratio should be used?

2026-06-23

Answer:
Yes, RNA and V(D)J libraries can be pooled and sequenced together.

Key considerations:

  • V(D)J libraries have a different fragment size distribution (~600 bp) 
  • V(D)J libraries typically require lower sequencing depth 

Recommended pooling ratio (molar):

  • V(D)J : 5' transcriptome = 1 : 10 

Additional considerations:

  • Maintain base composition balance across the pool 

Avoid duplicate index sequences within the same lane

 

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