What are you interested in with the co-factors? Do you have a specific question. If you do a dual x-linking ChIP-seq this would answer whether they are binding together and at what locations. So I would say it also depends on what you hope to learn.

Joshua Beytebiere thanks a lot. I am trying to investigate if my co-factors are really involved to regulate transcription factor ( mutated cell line). But now these co-factors have been found in both normal and selected cell line. So, I want to look if any other co-factors are involved now. That's my question.

Do you have any idea what these other co-factors might be? if not ChIP-seq would not really be possible if you don't know the protein of interest for the cofactor. At that point I would think about trying other methods.