PrepSCTFindMarkers

[Treshapdesai]

I have a merged object which is 32.5 GB. I am unable to SCTransfrom on merged object without crashing. Is my approach correct:

1. for Integrating 4 batches: SelectIntegrationFeatures, PrepSCTIntegration,FindIntegrationAnchors,IntegrateData, RunPCA, RunUMAP, FindNeighbours, FindClusters.
2. For annotating clusters: Set default assay to sct by looping through all objects in merged object. PrepSCTFindMarkers, FindAllMarkers?