Hello, I have 2 scRNA-Seq data set for 2 conditions. There is not any batch effect. Tissues, platforms, date of experiments are completely identical. Only difference is condition so if I do a batch correction, I would lose the information I need so I analyzed each data set seperately. I processed, clustered and identified cell types.
Now I want to to trajectory analysis of a specific cell type in both of the condition. To do that, I used subset function to create cell type specific Seurat object and merged them. After that, should I use counts data and start the analysis with Monocle 3 from the beginning or should I create CDS object with normalized data and directly order cells?
Thank you in advance.