I have a patient sample scRNA-seq data. Pre-treatment and Post Treatment for the same patient. The libraries were prepared on different days, of course because we treated the patient with the drug. The Pre and Post samples were sequenced at the same time in the same run. My question is should I need to perform the integration step (either by harmony or by seurat Integration step) to remove batch effects?

I do want to look at differences in the cells pre and post treatment, so I guess integration makes sense, since it will place similar cells (overlay) from different conditions (pre and post), but I am not sure.

I want to stress here (as I did in many posts before) that methods like harmony do a per-cell batch correction. This means the method aims to position each cell in a UMAP or in a clustering landscape as if there was no batch effect present. It does not do a per-gene correction, so you still cannot do differential expression analysis. It makes sense to do per-cell correction to remove unwanted technical variation. That enables to do clustering and dimensionality reduction between the samples, but you cannot run differential expression. The batch effect is still there and there is no method to maningfully remove this since treatment day and batch are confounded.