Library/ChIP preparation: What if my antibody has low binding affinity and there isn’t a better option available?

If when talking about low binding affinity you mean that the interaction between your protein of interest and its antibody is poor, you can try to make a library and sequence it but it is possible that the ChIP method is not appropriate for your protein/antibody pair. If you are worried about having a high background, you can test this and theoretically control for it by doing ChIP-seq in a cell where there should no binding. Please keep in mind that sometimes the inability to make a library is the result of a lack of antibody targets rather than an issue in library construction. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.