Control Types: Can we use any DNA-seq as an input sample?

DNA-seq processing is in many ways the same as an input sample. However, basic DNA-seq is done on naked DNA while input samples are crosslinked and sonicated while the chromosome structure remains intact. The other problem with using a random DNA-seq samples is that the purpose of the control is to correct for biases in the experiment. Some of these biases are technical, so it is optimal to make the input sample alongside the ChIP sample. However, anything you might want to do with a basic DNA-seq experiment can be done on an input sample. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde