How to integrate multiple single cell RNA-seq samples and perform pseudotime analysis by Monocle2

Question

[Issac]

Hi there,

I have 3 single cell RNA-seq samples and I would like to perform pseudotime analysis using Monocle2. I integrated these 3 samples together and normalized the merged dataset by SCTransform method with Seurat3 package. But this data can not be imported in Monocle2 cause the author said not normalize data yourself. I was wondering how to handle this case. Can Monocle2 remove batch effect just using log-transform and scale function? Thanks in advance for any suggestions and advices!

Best, Issac