Hello,

I want to ask a very general question. I am conducting ChIP-seq analysis. I know that every dataset is unique and has its own properties. Parameters during ChIP-seq is needed to adjusted to the datasets. However, I have spent a long time to understand and optimize the method of optimization . Now when I conduct the analysis on a dataset published in nature, the biological raplicates almost does not overlap at all. This is not a difference slight but it is like I am applying a wrong analysis pipeline for it. I am not sure where am I missing. Is there anyone facing the same problem and maybe advice me. Thank you.

Can you clarify:

Hello, I am doing the second one. I have taken the dataset from the analysis. And my results do not overlap with the results in the article. Thus, normally we expect biological replicates of a condition in chip-seq samples overlap for a larger fraction (compared to my venn diagram shown here). However, my results look like this.

It looks like I took samples treated with distinct conditions and expect them to overlap. However, these are biological replicates.

I hope I clearly explained my situation. Thank you.