An overview of Illumina multiplexing
Multiplexing Index 1 (i7) is always read. Index 2 (i5) is read only in dual index setting. Single indexing Dual indexing Single end (SE) R1, R2 R1, R2, R3 Paired end (PE) R1, R2, R4 R1, R2, R3, R4 Multiplexing - dual index reads - paired end