How to run ROSE by a wet-lab research

Question

[b8921019]

Hi, I am a wet-lab researcher and have zero experience in running bioinformatics software. Because I want to use ROSE to analyze super enhancers, I have tried to look for any online tool for super-enehancer analysis. However, I still don't know how to run ROSE. Can anyone share some step-by-step tutorials for this program? It would be much appreciated.

Answer 1

[ksong]

Hi my friend, I just figured it out.

1. I first downloaded the example data from this website: http://younglab.wi.mit.edu/super_enhancer_code.html
2. then I created python2.7 Conda environment on a linux computer.
3. I tried to run the example data and confirmed that it works.
4. I then ran ROSE for my own H3K27ac data

I had lots of problems initially and there was a hard time troubleshooting. Eventually I learned that it was because I did not do step 2) as the major python is python3 on our linux computer.