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Old 01-07-2017, 07:13 AM   #21
GenoMax
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Originally Posted by Shimul View Post
The Q30 is now 83.1% after 250 cycles, yesterday it was 96% after 70 cycles. But rest of the parameters are consistent: clusters PF 91.4%, cluster density 1092K/mm^2, which are the same as yesterday. Do you speculate anything? DO you think that the run will be okay?

Many thanks.

Shimul
Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out Q scores may keep dropping. Enjoy the weekend and don't worry about the run.

Last edited by GenoMax; 01-09-2017 at 07:51 AM.
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Old 01-08-2017, 03:27 PM   #22
kmcarr
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Originally Posted by GenoMax View Post
Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out the PF% will likely continue dropping as will the Q scores. Enjoy the weekend and don't worry about the run.
A correction Geno, %PF does not change. PF clusters are set at cycle 25. Q scores of course are calculsted on each cycle and later cycles always have lower quality than earlier ones.

Shimul, relax, your run is going fine.
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Old 01-08-2017, 05:41 PM   #23
nucacidhunter
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Originally Posted by GenoMax View Post
Sounds like this is your first ever run and you are anxious

Cluster density does not change over the run duration. As @nucacidhunter pointed out the PF% will likely continue dropping as will the Q scores. Enjoy the weekend and don't worry about the run.
I think it is less accurate quote of my post (#65) from the following:

http://seqanswers.com/forums/showthr...738#post202738
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Old 01-09-2017, 07:53 AM   #24
GenoMax
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Originally Posted by nucacidhunter View Post
I think it is less accurate quote of my post (#65) from the following:

http://seqanswers.com/forums/showthr...738#post202738
@nucacidhunter: Please accept my apologies. Thank you @kmcarr also. I should have checked my post more carefully (I have made necessary correction above).
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250 base reads, 500 cycle kit, cluster density, miseq, v2 hardware

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