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Can an entire index be N padded in Miseq Reporter?
Yes, N's are considered wild cards in MiSeq Reporter (MSR). For example, an index can be assigned "NNNNNNNN".
This is useful in the following cases:
- 1.Index quality may be low and N padding can help reduce loss of index fidelity
- 2.A run was setup as dual index but single-indexed samples were included in the loaded library. In this case, MSR will not be able to detect barcode collision between the two sample types.