Merging stringtie assemblies using stringtie merge

Question

[lakhujanivijay]

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.

Answer 1

[andrew.j.skelton73]

This depends on your hypothesis, but the idea generally is to merge all assembled transcriptomes, so that you have an "experiment-wide transcriptome", rather than stratifying.