Hi,
Are there ways to merge paired data before the model traning? I can merge ‘Gene Expression’ but not ‘peaks’ from multiple samples.
If your samples are using the same set of peaks it should be equivalent to merging genes.
If they aren’t, then the merge needs to happen upstream of scvi-tools, by re-calling peaks across samples, or merging the peaks and remapping each sample to the set of merged peaks.
If this is 10x data you can use cellranger aggr functionality or other pipelines like ArchR to do this, then use the resulting peak-by-cell matrix in scvi-tools.