Pseudo time analysis with monocle3 of the data with Day 1 and Day 2 samples for Control and Disease.

[SMP7UC]

Hi,

We collected scRNAseq data from Day 1 and Day 2 of each control and disease sample. I ran the monocle3 workflow on each of the samples separately, by condition (control and disease), and by Condition and Day (Control Day 1, Control Day 2, Disease Day 1 & Disease Day 2) as well. For different approaches, I got different results for the tracks and endpoints of pseudo time. Finally, we decided to do it based on condition (Control and Disease). I did not find anything about which approach I should go for in this case. If anybody has any idea about it, please let me know. It would be very helpful for me to be assured that I am doing everything right. FYI, before applying monocle3, I applied the usual workflow to get the clusters.

Feel free to ask if you need any other information about it.