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Old 04-08-2015, 11:09 AM   #1
pmiguel
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Default How many HiSeqs still run a control lane?

A "control lane" is a lane of phiX library -- if I understand correctly it was required back in the "GA" days. Kind of a "tithe" to the gods of sequencing. One lane of eight set aside to honor them. (Joking...)

I was a little late to the Illumina scene. By the time we started running it was not necessary to run a control lane, although you could. So I think we've run 1 control lane in the last 3 years.

Anyone still running them?

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Old 04-09-2015, 05:17 AM   #2
Jessica_L
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When I was working in a core lab up till about May of 2013, we were running them religiously. I'm not sure if my old lab has changed their workflow in the time I've been gone, even though Illumina has made it pretty clear that you no longer need so much PhiX.

Short answer: I was running them up till about two years ago.
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Old 04-09-2015, 05:50 AM   #3
kmcarr
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With recent versions of the software it is not possible to designate a control lane.

From the HiSeq Control Software v2.2.38/Real Time Analysis v1.18.61 Release Notes (July 2014):

Quote:
I. HCS v2.2.38
FEATURES:
Control lanes are no longer required
  • The control lane option has been removed from all run modes: internal testing by Illumina has shown that a control lane is unnecessary when using RTA 1.18.61, which includes new features to support low diversity sequencing. See the RTA 1.18.61 section (below) for more details. When sequencing challenging samples such as a single amplicon, a 10% PhiX spike-in is recommended in place of a control lane.
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Old 04-09-2015, 06:22 AM   #4
MU Core
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Our procedure is to now include a 0.1% spike-in of PhiX to each lane for run performance monitoring and troubleshooting.
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Old 04-09-2015, 08:12 AM   #5
pmiguel
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Quote:
Originally Posted by kmcarr View Post
With recent versions of the software it is not possible to designate a control lane.

From the HiSeq Control Software v2.2.38/Real Time Analysis v1.18.61 Release Notes (July 2014):
Good point. I did see that. But it didn't make much of an impression since we never run one anyway...

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Old 04-26-2015, 06:47 PM   #6
ETHANol
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As mentioned with the new base caller you cannot even specify a control lane if you want to. We do a lot runs that are only whole genome bisulfite sequencing so we use to have to do a control lane, now obviously we don't. We spike in PhiX at 5-10%. The official word from Illumina is you need 10% PhiX, but the unofficial word is that you can go as low as 5% PhiX. We've gone as low as 2.5% and the data still looked good, but we target 5-10%.
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Old 04-27-2015, 08:49 AM   #7
pmiguel
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Quote:
Originally Posted by ETHANol View Post
As mentioned with the new base caller you cannot even specify a control lane if you want to. We do a lot runs that are only whole genome bisulfite sequencing so we use to have to do a control lane, now obviously we don't. We spike in PhiX at 5-10%. The official word from Illumina is you need 10% PhiX, but the unofficial word is that you can go as low as 5% PhiX. We've gone as low as 2.5% and the data still looked good, but we target 5-10%.
Thanks Ethan.
Hey, I thought you got tired of doing science in Greece and had left?

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