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

memento · 01-22-2013, 08:58 AM

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 · 01-22-2013, 10:13 AM

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 · 01-22-2013, 12:00 PM

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

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01-22-2013, 08:58 AM	#1
memento Member Location: UK Join Date: Nov 2010 Posts: 49	Can You mix indexed with un-indexed library on MiSeq run ? 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!

01-22-2013, 10:13 AM	#2
kcchan Senior Member Location: USA Join Date: Jul 2012 Posts: 184	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.

01-22-2013, 12:00 PM	#3
memento Member Location: UK Join Date: Nov 2010 Posts: 49	Thanks! Trimomatic should be able to recover these ( I hope!).