I have a set of 2 transcriptome samples
Sample1 - A. control B. treated
Sample2 - A. control B. treated
I assembled the transcriptome using stringtie
Objective is to compare A vs B for sample1 and A vs B for sample2.
How should I merge the assemblies using
stringtie --merge ?
Should I merge assemblies separately for sample 1 and sample 2 or both of them together?
i.e. while running
stringtie --merge, should I run in twice; once with a mergelist.txt file for sample1 and then for sample2.