Question: Can I use aggr to combine 3’ LT v3.1 data with standard 3’ v3.1 data? Will there be chemistry batch effects?
Answer: The cellranger aggr pipeline supports the aggregation of Single Cell 3’ LT v3.1 (LT) data with the standard Single Cell 3’ v3.1 data.
We observed no noticeable batch effects during internal testing when aggregating LT and 3’v3.1 data with well-matched input material. We recommend starting with cellranger aggr without chemistry batch correction. If the results reveal obvious differences between the LT vs. 3’v3.1 data, you can try cellranger aggr with chemistry batch correction, which may improve the mixing of the batches in the t-SNE visualization and clustering results.
If you are aggregating LT samples with other chemistries (3’v2, 5’v2, etc.), you can treat LT similar to 3’v3 chemistry. For example, we recommend using chemistry batch correction when aggregating 3’v3 (standard or LT) with 3’v2 chemistry. More information can be found in this knowledge base article: Can I aggregate gene expression data from different chemistries?