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Old 01-22-2013, 10:13 AM   #2
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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.
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