Toilet trouble when flushing the downstairs toilet it makes a terrible noise and again when the cistern refills

Based on the phrasing of your question, I'm thinking that the bad noise happens for the first time when the valve opens to start filling (this happens when you first let water into the bowl) and then again when the valve closes (when the cistern is full). Valves sometimes have a high-pitched squealing noise when it takes a long time to open or close this valve. Sometimes, you can make it go away by turning the screw to adjust the height that the ball/float has to be in order to shut off the water (the more horizontal, the longer it takes to shut off the flow, and the longer the noise continues). Sometimes, this is just caused by an aging mechanism and it turns out to be quicker and easier to just replace that part of the toilet (they make replacement kits that are very inexpensive and easy to install).