Hi! I have a question about something similar. If I have 3 control and 3 treatment samples, each of one corresponding at a time point (24h 72h and 120h). How do you recommend to run strigtie? 1- If I want to compare in the differential expression analysis control and treatment in each time point do I need to run stringtie for transcripts assembly, then merge only control and morphine samples for each time point (so I will have 3 merged files) and finally use each merged time point file as a reference for control and treatment when rerunning stringtie? 2- Or if I want to compare control and treatment samples along time (comparinssong between six samples) do I need to merge all six samples and then use this unique merged file for transcripts abundance estimation?
Finally is there any option to run ballgown for comparisson of the 6 samples along time? or ballgown only does comparisson between two groups?