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.
1) I calculated overlap regions of normal and tumor samples separately first. After that, I compared two groups. This is my high confidence peaks.
2)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.