Hello,
I've used Seurat to analyse my scRNAseq data, which then I've converted into a Monocle CDS using SeuratWrappers to study the pseudotime trajectories by Monocle3b(v0.2.2.0). I have different conditions (different developmental ages that clustered together) within the same partition. I would like to know if it's correct to divide the Seurat object into 1 object/condition prior to convert them into different Monocle CDS and so analyse their trajectories separately to be able to compare them. As far as I know, this means that I impose the same low-dimentional reduction shape (such as UMAP) to the diferent conditions, so I was wondering if the program will result in trajectory artifacts.
yamihn
commented
1 year ago
Hello, I've used Seurat to analyse my scRNAseq data, which then I've converted into a Monocle CDS using SeuratWrappers to study the pseudotime trajectories by Monocle3b(v0.2.2.0). I have different conditions (different developmental ages that clustered together) within the same partition. I would like to know if it's correct to divide the Seurat object into 1 object/condition prior to convert them into different Monocle CDS and so analyse their trajectories separately to be able to compare them. As far as I know, this means that I impose the same low-dimentional reduction shape (such as UMAP) to the diferent conditions, so I was wondering if the program will result in trajectory artifacts.
Any help will be welcome! Thanks