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2 hours ago by

I did ChIP seq using H3K27ac antibody to quantify super enhancer regions in normal vs breast cancer cells. I ran ROSE algorithm on normal mammary epithelial cells and breast cancer cells to get a list of super enhancer regions in each cell line. I have a list of super enhancer regions for both and I want to compare super enhancers between the two outputs I got. How would i compare the two lists and see if they have super enhancer regions that overlap or not to analyze acquired/lost super enhancers between the two cell lines. I know bedtools intersect might be able to do it, but am confused about the command I would input to compare the two files. Any help is appreciated. Thank you



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