MultiVI questions on Integrating Multiple Multiome Datasets

General Multiome
1

Hi all, I have a couple of questions regarding the tool. First, thank you for providing both the tool.

  1. For multiple multiome samples, is it better to use Cell Ranger aggr without normalization to integrate modalities and samples, or to process each sample’s matrix individually?

  2. I’d like to use raw data for MultiVI, perform QC in Seurat, and then integrate the MultiVI latent space embedding. Would this be the recommended approach?

Additionally, are there papers that have used MultiVI for integrating multiple multiome samples with the code shared or example? And finally, how can we best assess whether sample and modality integration has been successful, within this framework?

Thank you