Mixing indexed and no-indexed lib in a same MISEQ run

[MARIAC]

Hi, It is possible to run on a single Miseq RUN (v2, 2x150bp) libraries with illumina index (up to 16 index on I5) and libraries without index (I'll could retreived the latest in the undeterminated file).

If it's possible is there a ratio between these two kind of libraries I have to follow ?

Thanks for anwsers,

Cédric

[SNPsaurus]

My lab sometimes runs, on a HiSeq, multiple different libraries of which some are indexed and others not. Problems can occur if the number of indexed clusters is low within the lane. One issue is that clusters that lack an index will get called as having the index of a nearby index. The index quality suffers as well. I'd try to get the index library up to 50% of clusters, but 30% will work somewhat well depending on cluster density.

MiSeqs may be different, but I thought I would chime in anyway!

[cmbetts]

It certainly can be done, as long as you either have a clear way to filter for the non-indexed library or are willing to tolerate contamination of your indexed libraries in the non-indexed one.
I generally expect >99.5 of my indexed reads to get properly assigned, which means you can expect ~100k unassigned reads to leak over. It depends if this is a deal breaker for your experiment or not.