Correlation for ATAC-Seq and Chip-Seq
Hello, Can somebody help me on how to find a correlation between ATAC-Seq and Chip-Seq? I have MACS2 output for ATAC-Seq and Chip-Seq. I also need to find a correlation between RNA-Seq and ATAC-seq/Chip-Seq. Thank you
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In the end, what you need to do is to associate ATAC-seq peaks with gene expression. That can be by proximity, by similar patterns between gene and chromatin read counts, or by anything else. I have yet to see an accepted, universal and validated approach for it. Everyone does their own thing. It's a mess. Usually it's either proximity or a combination of proximity and expression patterns. Can you add details?
I have submitted a paper in which I have shown, using ATAC-Seq and Chip-Seq, that some of the genes have lost chromatin accessibility and the same genes are downregulated. They asked us to show a correlation between ATAC-Seq, Chip-Seq and RNA-Seq.
Great, so you have your matching already. What is the problem one can help with?
I want to find a correlation between ATAC-Seq, Chip-Seq and RNA-Seq