Originally posted by westerman
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Just got 10.3Gbp raw data, histogram suggested 7.0Gbp >Q30 by end of 251|6|251 run. Useable sequence (post-QC trim) checking it on Genomics Workbench probably closer to 9Gbp. About 39.5M reads with average length of 225bp.
Cluster density of 1300K/mm2 - same library gave ~3.5Gbp on a v1 flowcell with 2x151bp reads (clustered at 8pM).Last edited by matth431; 03-05-2013, 04:44 AM.
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Hi All,
I am finally running of my bacterial pooled DNA library (which I made using Nextera XT) on the Miseq using MiSeq V3. I have checked the machine now and it shows that after 70 cycles, the >=Q30 is 96%, cluster passing filter 91.4%, and the cluster density is 1092K/mm.
Do you think that the run is going well?
Hope to hear back from you soon again!
Cheers,
Shimul
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Originally posted by Shimul View PostHi All,
I am finally running of my bacterial pooled DNA library (which I made using Nextera XT) on the Miseq using MiSeq V3. I have checked the machine now and it shows that after 70 cycles, the >=Q30 is 96%, cluster passing filter 91.4%, and the cluster density is 1092K/mm.
Do you think that the run is going well?
Hope to hear back from you soon again!
Cheers,
Shimul
--
Phillip
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Originally posted by pmiguel View PostSure, those metrics would consistent with the start of a good run.
--
Phillip
Many thanks.
Shimul
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Originally posted by Shimul View PostThe 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
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, 08:51 AM.
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Originally posted by GenoMax View PostSounds 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.
Shimul, relax, your run is going fine.
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Originally posted by GenoMax View PostSounds 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.
http://seqanswers.com/forums/showthr...738#post202738
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Originally posted by nucacidhunter View PostI think it is less accurate quote of my post (#65) from the following:
http://seqanswers.com/forums/showthr...738#post202738
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