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.

See Illumina Knowledge Article Using an N wildcard in index sequences in different Illumina FastQ generation software for more information.

For any feedback or questions regarding this article (Illumina Knowledge Article #3624), contact Illumina Technical Support [e-mail].