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Old 01-22-2018, 09:24 AM   #21
misterc
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http://enseqlopedia.com/2016/10/inde...-phix-control/
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Old 01-24-2018, 11:15 PM   #22
HeinKey
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perhaps this question is asked before, but I don't understand the added value of dual indexing over single indexing anymore if both indices are unique in dual indexing. The highest possible complexity is then equal to highest complexity of single indexing.
What do I miss?
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Old 01-25-2018, 12:15 AM   #23
nucacidhunter
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Quote:
Originally Posted by HeinKey View Post
perhaps this question is asked before, but I don't understand the added value of dual indexing over single indexing anymore if both indices are unique in dual indexing. The highest possible complexity is then equal to highest complexity of single indexing.
What do I miss?
Your statement is correct but UDI addresses another issue (index hopping) in patterned flow cells used in HiSeq 3000/4000 HiSeqX and NovaSeq to maintain fidelity of reads assigned to multiplexed libraries. Links in post #1 should give you some information on the issue.
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Old 01-25-2018, 07:52 AM   #24
Innovelty
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Sometimes, especially on the new Illumina flowcells, the indices get swapped around onto molecules they didn't originally belong to. With non-unique dual indices, where any combination of the index pool is potentially valid, that problem is invisible -- some of your reads *actually* belong to one library but have the indices for another library. With unique-dual-indexing, the problem still occurs, but it's not invisible -- any index-hopping or index-swapping will result in a read with an invalid combination of indices, and so it'll get kicked to the "Undetermined" set. You still "lost" that read, but it didn't get erroneously assigned to a different library.

Unique-dual-indexing *is* basically single-indexing, but you've got two barcodes, and the likelihood that both barcodes get swapped to something valid is practically nil.
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