# Pseudotime analysis on multiple samples

I am using Monocle3 to run pseudo time analysis on samples at two different conditions (samples are paired). My question is, is it valid to combine all the cells from samples at specific condition when clustering, learning graph and ordering cells? or should I pick up only one sample per condition and run the analysis on?

My understanding is that pseudotime analysis uses the expression data of cells to try to infer the trajectory of cells, so I believe it might not be correct when I pool all the cells that might not have a true trajectory?

Thanks