Hi ;) I think it depends on the binding of your protein of interest. If it binds efficiently to many places within chromatin, then there is a chance that you will see both, ChIP and RNA reads. If not, then probably you will see mostly RNA reads. Also, it depend on the no. of reads that you can get on the specific sequencer. However, to be honest, to get nice results and proper depth, I wouldn’t run them together.
Es dependiente de la unión al sitio de la proteína de interés. Particularmente de la cromatina. Desde este lugar deriva o no en lecturas fallidas de ARN.