Question: Merging stringtie assemblies using stringtie merge
0
gravatar for Vijay Lakhujani
4 days ago by
India
Vijay Lakhujani560 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 4 days ago by Vijay Lakhujani560

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 REPLYlink written 4 days ago by andrew.j.skelton733.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1797 users visited in the last hour