Where does the read start?

[Ingeneious]

The read starts reading the index, then the target specific primers and then the insert itself, correct?

So for example, I am using a 100 cycle kit, my index is 8bp long and I am doing 50bp PE reads, how much of my target insert would actually be sequenced? 92bp?

[blancha]

The index has a distinct primer, and is sequenced separately.
50 bases will be sequenced from both ends of your insert.
I think there is a total of 108 cycles, to sequence the index in addition to the insert.

[microgirl123]

Nope. You will sequence 100 bp of your insert (50 in each direction). The index is primed, sequenced, and read separately.

[Ingeneious]

Great, thanks.