I got chip seq peak results with bed format. There are 7 normal vs 13 tumor samples. I have two consensus peak results from this data.
- I calculated overlap regions of normal and tumor samples separately first. After that, I compared two groups. This is my high confidence peaks.
- I piped merged all normal files and tumor files into separate bed then, calculated the overlaps. This is my low confidence peaks.
I wanted to show that 1st one is part of my 2nd group statistically. I decided to apply t test but I couldn't figure out a way to implement it to bed files. Could you show me way to do that?
Thank you for your help.