Clarification about how mapping to a reference genome works in RNA seq When mapping reads to a reference genome, how is it possible to tell which part of the genome the read is referencing if the genome possibly has the same repeated sequences in different areas? What I mean by this is let's say for the sake of argument that you have a read "AGCTAGCT". If the reference genome has two places where the sequence "AGCTAGCT" is present, how do we tell which one it's coming from? I'm assuming that the length of the read is chosen long enough such that this doesn't happen but perhaps I'm wrong?
You can't always know exactly where every read originated, even if you use long reads to sequence full-length transcripts (odds are there's at least one transcript that's duplicated in the genome). This is also not exactly a problem, such reads can either be discarded or reported as multimapping.