Can You mix indexed with un-indexed library on MiSeq run ?

[memento]

Would it be possible to mix indexed (8nt index for 16 samples) with un-indexed library (eg Rohland et al 2012 trimmed adapters) to run on the same MiSeq run ? Would the unindexed reads endup in unrecognized bin/unaligned bin (less of a problem) or clusters would not be registered - the run would have to be set to a indexed mode, to read the indices (my guess).
Thanks in advance!

[kcchan]

The unindexed library should end up in the undetermined file. However, that file will also contain a small percentage of other reads including mismatched indices and PhiX if you added any in. It may be better to re-queue the analysis a second time with the sample sheet containing all Ns to filter out all indexed reads, leaving only the unindexed library in the undetermined single file.

[memento]

Thanks!
Trimomatic should be able to recover these ( I hope!).