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Old 01-16-2015, 03:15 PM   #1
Ingeneious
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Default Dual-index vs single index

What would be the benefit from using 2 x 8bp dual indexes vs say... 1 x 16bp single index for a paired end read?

Last edited by Ingeneious; 01-16-2015 at 04:07 PM.
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Old 01-16-2015, 04:26 PM   #2
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One good reason is to identify barcode swapping between samples that can happen during PCR:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245947/
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Old 01-16-2015, 09:27 PM   #3
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How many adapters or primers would you need for each of those scenarios to identify a given number of samples?
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Old 01-19-2015, 10:34 AM   #4
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Quote:
Originally Posted by atcghelix View Post
One good reason is to identify barcode swapping between samples that can happen during PCR:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245947/
Thanks, this makes sense. According to the paper, it looks like contamination is also an issue, if you pool after PCR.
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Old 01-19-2015, 11:22 AM   #5
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I think SNPsaurus's point is more important, however. You can get by with far fewer distinct adapters by using the combinatorial aspects of a two-index system.
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