Question: Merging stringtie assemblies using stringtie merge
gravatar for Vijay Lakhujani
7 months ago by
Vijay Lakhujani1.3k
Vijay Lakhujani1.3k wrote:

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.

ADD COMMENTlink written 7 months ago by Vijay Lakhujani1.3k
gravatar for andrew.j.skelton73
7 months ago by
Newcastle Upon Tyne
andrew.j.skelton734.1k wrote:

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.

ADD COMMENTlink written 7 months ago by andrew.j.skelton734.1k
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