I used 2 RNases, RNase A and RNase T1. These samples were also run on a sucrose gradient, and only the monosome peak was taken. Perhaps that is why it's much lower? I was following an older Ingolia paper that said there may be very short ~15 nt footprints. Periodicity for these samples is suboptimal until 29nt (phase score 0.92), 30nt (.95), 31 (.85), with smaller nt ranging from (.13 to .75) Is it best practice to filter tRNAs as well via SortMeRNA?