Why is it that when doing paired end Radseq that R1 and R2 have different start points? For instance, while doing Radseq you do a restriction digestion of your DNA using enzyme X- shouldn't the sequencing reaction take place from either end of where the enzyme cut? If it doesn't- but happens randomly where do your multiplex sequences go?
For instance- if you are sequencing the sequence on an illumina machine with the "<>" representing the cut site-
Where does the sequencing reaction start from in each direction?
Where does the multiplexing sequence go? - does it go on each?