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.
miseq index 5' TCTTTCC 3' >>>>>>> 5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTT 3' ^------------------^ ^--------------------^ flowcell binding seq adapter-binding seq
When we sequence these libraries dual-indexed on the MiSeq, the machine reads into the adapter and returns the index sequence
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?
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.