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Old 10-24-2017, 05:31 PM   #3
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Join Date: Feb 2008
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Some of the samples had essentially zero reads after demultiplexing. We also found discarded reads where over a million had the same index.
Possibility of an unbalanced pool/failed samples in addition to the index sequence errors. You can't fix the former but latter should be easily fixed by using correct indexes and redoing the demultiplexing as suggested by @nucacidhunter. You should always use the entire set for demultiplexing when using a corrected samplesheet.
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