Bait Coordinates don't intersect with .rmap file

[Former user]

I'm new to capture HiC analysis so I'm assuming that I'm just doing something wrong. I have what I believe to be the bait coordinates and I've also used hicup_digester to create the .rmap file following the arima protocol. However, when I then intersect my bait coordinates with the .rmap file using dplyr::inner_join in R, I get ZERO overlap. I'm not really sure what to do! I've also tried the create_rmap_baitmap.pl script from chicagotools but kept getting error messages. Any help would be greatly appreciated! Thanks