RNA-seq samples along different time points, how to run Stringtie?

Question

[iraia.munoa]

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?

Thanks!

Answer 1

[grant.hovhannisyan]

I would run Stringtie for all the samples separately, then will merge all the GTF files together and will use that merged GTF file to count the reads using featurecounts. Then you can perform a time-series dif. expression analysis with DESeq2 for example.