A method of separating bead substrates includes applying an emulsion to an emulsion-breaking solution. A dispersed phase of the emulsion includes an unbound polynucleotide, a first set of bead substrates and a second set of bead substrates. The unbound polynucleotide includes a segment complementary to a coupling oligonucleotide. The first set of bead substrates includes the coupling oligonucleotide extended to include a segment complementary to a portion of the unbound polynucleotide. The second set of bead substrates includes the coupling oligonucleotide. The emulsion-breaking solution includes an interference probe having a sequence similar to the coupling oligonucleotide or complementary to the coupling oligonucleotide. The method further includes binding beads of the first set of bead substrates to separation substrates and separating unbound beads of the second set of bead substrates from the beads of the first set of bead substrates bound to the separation substrates.