# What i5 index should I use on the Illumina sample sheet for an unindexed p5 primer?

I have an upcoming run on a HiSeq X and most of the libraries in the pool have both i5 and i7 indices. However, some of the libraries were made with the IS4 p5 oligo and it is unindexed.

The IS4 indexing oligo is from the following paper. The sequence is below.

Meyer, Matthias, and Martin Kircher. "Illumina sequencing library preparation for highly multiplexed target capture and sequencing." Cold Spring Harbor Protocols 2010.6 (2010): pdb-prot5448.

                                 miseq index
5' TCTTTCC 3'
>>>>>>>
5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTT 3'
^------------------^         ^--------------------^


When we sequence these libraries dual-indexed on the MiSeq, the machine reads into the adapter and returns the index sequence TCTTTCC.

## Question

What will the index sequence be when the HiSeq reads it?

The more fundamental question is: How exactly do MiSeq and HiSeq machines read index sequences?

### side note

Here is what an index p5 and unindexed p5 molecule look like:

Update: Sept 2019 - After running into this problem again, an Illumina representative agreed with Devon Ryan and said that setting up a run for single indexing is the best option when there are unindexed p5 ends on one or more libraries.