SCT+Harmony

[fafuyyk]

Hello!
Thank you for the single cell tutorial, but I encountered some problems while learning the tutorial. I encountered problems when I used SCT+merge+Harmony for normalization. Let me first introduce the general situation. I have two samples, each of which was SCT standardized as a Seurat object, and then merged using merge. The specific parameters are:

merged_seurat <- merge(x = norm_seurat_list[[1]],
y = norm_seurat_list[[2]],
merge.data = TRUE)

The default matrix of norm_seurat_list[[1]] is SCT.

After merge, I think there should be only one counts in the RNA slot, but there are actually two, counts.1 and counts.2, which affect the counts of the two Seurat objects. This affects my subsequent analysis. I will use the RNA slot for analysis later. I want to know how to solve this problem.