is MultiVI suitable for integrating ATAC and RNA assays from 10X Multiome?

[MolendoLabBio]

Hi,

I have several Multiome libraries from pooled samples (we have 6 patients per libraries and pooled 4 libraries per modality for sequencing). Our lab was planning to demultiplex the pools using genotyping data and Demuxafy. We would then pre-process the ATAC and RNA data separately before using MultiVI to integrate the two modalities. Is this feasible?

I read on here that MultiVI is designed for integrating multiome with either ATAC or single-cell RNA data but not really for integrating ATAC and RNA from the same multiome experiment. However, this page from sc best practices shows that the two assays can be concatenated before using MultiVI (https://www.sc-best-practices.org/multimodal_integration/paired_integration.html#multiome-data).

Does anyone have experience integrating the modalities using scvi tools?

We are aware of Signac but would like to try with MultiVI if possible.

[canergen]

Hi, joint alignment and demultiplexing into patients is better (higher number of reads and SNPs per cell). Please check with demuxafy for code. You can then run multiVI on these cells with both RNA and ATAC assayed. We prefer usage questions on discourse.