MiSeq wet lab SOP

Theory behind mothur
1

Hi,

I have a question about the dual-indexing method (Kozich et al.). I have gotten a bit confused about the indices.

Am I right in thinking that the index (i5) on the forward PCR primer is index 1? Is it sequenced first? Or is the index (i7) on the reverse primer index 1? The sequencing centre that we are using have asked for the index 1 and 2 sequences.

Thanks for your help.

edit: I think it’s the other way round actually isn’t it?

2

I think i7 is index 1 and i5 is index 2:

http://res.illumina.com/documents/products\technotes\technote_nextera_low_plex_pooling_guidelines.pdf