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 situations:

1. Index quality is 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 does not 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].