Can someone confirm that the index to enter in the sample sheet for PhiX V3 demultiplexing is TTAGGC (IDX3, as read)? Got 30G "undetermined indices" on control lane.
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Originally posted by westerman View PostIndex #3 is indeed TTAGGC
How many other indexed reads did you have in the control lane? Or was that the only one?
I realize now it failed because it was the only index and we should have left the index field empty. But if we do want to use it for spike in, we need to know its index.
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Originally posted by HMorrison View PostCan someone confirm that the index to enter in the sample sheet for PhiX V3 demultiplexing is TTAGGC (IDX3, as read)? Got 30G "undetermined indices" on control lane.
Simply reading the %Base graph for our control lane though the index appears to be GTATGC. What is odd is that this sequence appears downstream of the index in all of the TruSeq adapters.
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Originally posted by kmcarr View PostWow, I was just looking for this information myself this morning. I haven't found an authoritative source yet though. I highly doubt that Illumina would use an index sequence from their library prep set though; that would preclude being able to use that index for one of your samples if you wanted to spike in some phiX.
Simply reading the %Base graph for our control lane though the index appears to be GTATGC. What is odd is that this sequence appears downstream of the index in all of the TruSeq adapters.
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Originally posted by hoisinjl View PostI talked to techsupport the other week, and PhiX v3 does not contain an Index. Only if multiplexing PhiX is indexed with index #3. This version of PhiX is no longer being made or sold.
PE-400-2002 | Multiplexing Sequencing Primer and PhiX Control Kit v2.0 (10 flow cells)
Wouldn't that have bar coded PhiX in it?
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Phillip
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