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Old 05-06-2015, 12:20 PM   #1
Dr. Hybe
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Default Anyone had success with Illumina V2 Rapid 2x250?

Our institute is having trouble completing these long runs. They seem to die towards the end of both reads, camera goes out of focus, etc. They are being run on an upgraded HS2000. FYI, the samples all passed on MiSeq 2x300. We are looking for slightly more yield meta, amp.Has anyone had similar issues, any success, any advice?
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Old 05-06-2015, 01:20 PM   #2
dpryan
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I guess it depends on how good of success you're after. We had a 2x250 v2 rapid run finish this morning and the results were relatively good. There was decreased quality toward the end of each read, but this was due primarily to two tiles (I think they were the exact same ones for each of the reads), so it turned out that the vast majority of reads were quite good. I should note that there was a bigger issue with the end of read 2, where a large block of tiles had problems. The latter issue combined with the same tiles showing some quality problems in both read 1 and 2 would be compatible with a camera problem, since there was an obvious per-tile difference...thereby suggesting that the problem isn't due to the chemistry itself.

I can't give any advice, as I don't personally deal with the sequencer, but that's at least the sort of thing that we're getting at the moment.
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Old 05-06-2015, 01:22 PM   #3
GenoMax
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With an n=1 we had no problems. Got about 250M reads per lane.
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Old 05-07-2015, 06:52 AM   #4
Dr. Hybe
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Are you guys using a native 2500 V4 capable instrument, or an older upgraded 2000?
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Old 05-07-2015, 07:19 AM   #5
GenoMax
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Our run was on an upgraded older 2000.
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Old 05-08-2015, 07:54 AM   #6
pmiguel
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Quote:
Originally Posted by GenoMax View Post
With an n=1 we had no problems. Got about 250M reads per lane.
So, 125M pass filter clusters per lane, right?

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Old 05-08-2015, 08:07 AM   #7
GenoMax
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Quote:
Originally Posted by pmiguel View Post
So, 125M pass filter clusters per lane, right?

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Correct. ~140 M per lane. 79% > Q30.
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Old 05-28-2015, 07:14 AM   #8
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I hope the problem has been solved by now!
Anyway: With 2 native HS2500 we regularly get >300M cpf per flowcell and between 80 and 85% Q30 for amplicon data.
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Old 05-29-2015, 06:15 AM   #9
Dr. Hybe
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We've given up for the time being in favor of V1 rapids. Our instrument is an older one that we bought in 2011 and then upgraded to 2500. We're thinking that the camera/optics aren't capable of running 500 cycles?
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