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Old 01-17-2018, 10:47 AM   #12
Innovelty
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Location: Storrs, CT

Join Date: Sep 2012
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Thanks for bumping this thread up again, systembio.

From what I know about the MiSeq chemistry (and it was the first sequencing platform I used) the unique dual indices shouldn't be a *problem* for MiSeq. Libraries made with UDI will sequence just fine on a MiSeq. They're unecessary, because MiSeq does not have the index-hopping problem that the HiSeq does, because the MiSeq's cluster-formation process is different. But definitely doing a little MiSeq nano run of your libraries to make sure they're what you wanted would be fine, prior to a HiSeq run. (If I'm wrong about this, though, I am sure someone will correct me!)

To answer my own question from a few months ago, the barcodes must be unique at both ends, but they don't have to be "the same index" at each end. Just each p5 index can only be used once, and each p7 index can only be used once, so each library gets a unique PAIR of indices. (Since I was struggling with it awhile back, I think I might as well clarify it for anyone else.) We ended up sequencing at Berkeley's genomics core, and they sell plates of UDI. Very pleased with them.

Last edited by Innovelty; 01-17-2018 at 10:49 AM. Reason: Needed to add clarification
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