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Old 09-27-2011, 04:56 AM   #1
HMorrison
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Default PhiX index

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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Old 09-27-2011, 06:24 AM   #2
westerman
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Index #3 is indeed TTAGGC

How many other indexed reads did you have in the control lane? Or was that the only one?
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Old 09-27-2011, 06:29 AM   #3
HMorrison
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Originally Posted by westerman View Post
Index #3 is indeed TTAGGC

How many other indexed reads did you have in the control lane? Or was that the only one?
I know IDX3 is TTAGGC, but is that the index used for PhiX control, version 3?
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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Old 09-27-2011, 06:35 AM   #4
kmcarr
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Quote:
Originally Posted by HMorrison View Post
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.
Wow, 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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Old 09-27-2011, 06:41 AM   #5
HMorrison
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Originally Posted by kmcarr View Post
Wow, 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.
They did use IDX3 before this; we verified that when we were using earlier kits and Casava 1.7 where we could actually look at the index reads. Now with 1.8, I can't do that. I may have to go back and run with 1.7.
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Old 09-27-2011, 12:35 PM   #6
hoisinjl
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I 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.
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Old 09-28-2011, 06:09 AM   #7
pmiguel
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Originally Posted by hoisinjl View Post
I 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.
What about:

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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