I am trying to solve my curiosity regarding repetitive element transcription but I can't directly map on highly repetitive elements because multi-mapping issue. So I just wondering if it's possible to extract "unique" reads from RepeatMasker, let's say Alu for example and allow certain degree of mismatches, in order use the result as a reference genome. What do you think, is it easily feasible? (I don't have a great computational skills)
Any input is more than welcome!