Mixing dual and single index TruSeq samples in a single MiSeq run

[pmiguel]

Should be possible, right? What happens if you specify both in a sample sheet?

I presume that if you specify a mixture of 6 and 8 base indexes for index1 that the instrument will do 8 bases. Then a mixture of 8 and zero base indexes for index1 should also give the desired result.

[Vinz]

I would extend the 6 bases of index 1 to 8 bases. The 2 bases after the index are known...
Likewise I would also give the 8 bases of the adapter for the single index samples. That way you do not rely on the software to be very advanced...