Originally posted by pmiguel
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Using High output we are actually getting over 500 million reads per run. Unlike our GAII, and HighSeq, we actually have to pay very close attention to cluster density. The target cluster density for high quality samples is 1.75pM-2pM. Anything above and below will results in under/over clustering. So your samples need to be very exact with concentration.
These are solely made to be streamlined with the BaseSpace. Right now it only works with BaseSpace onsite, not in the cloud as they are having some majority broker issues that still are not resolved. Make sure you do your research in regards to output files and data in regards to basespace because it is not a visual machine. It gives you the output files and you must use 3rd party software on a different computer to view the results. Very annoying.
Overall very impressed with the NextSeq's, not so much BaseSapce.
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Originally posted by williamhorne View PostUsing High output we are actually getting over 500 million reads per run. Unlike our GAII, and HighSeq, we actually have to pay very close attention to cluster density. The target cluster density for high quality samples is 1.75pM-2pM. Anything above and below will results in under/over clustering. So your samples need to be very exact with concentration.
These are solely made to be streamlined with the BaseSpace. Right now it only works with BaseSpace onsite, not in the cloud as they are having some majority broker issues that still are not resolved. Make sure you do your research in regards to output files and data in regards to basespace because it is not a visual machine. It gives you the output files and you must use 3rd party software on a different computer to view the results. Very annoying.
Overall very impressed with the NextSeq's, not so much BaseSapce.
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Also what kind of connectivity does the thing have besides networking? Since it's targeted at mid-level labs and not large facilities, it won't always be in pipelines that immediately dump everything to a computing cluster, let alone BaseSpace. I just ran a month-old MiSeq yesterday that's not even networked (though we don't have gigabit ethernet so fat lot of good that would do anyway) and I had to copy out my data through a USB2.0 port - what year is this? So with NextSeq-scale data volumes, this matters.
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Originally posted by jwfoley View PostAre you tied to Basespace for data management, or is there a way to copy to a networked drive (either as the run is being performed or after the run has finished)? I'd like to understand a little bit more about how the data is moved around.
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With all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.Last edited by nucacidhunter; 05-16-2014, 04:27 PM.
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Originally posted by nucacidhunter View PostWith all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.
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Originally posted by nucacidhunter View PostWith all discussions in this thread I wondering if there will be any issue if I spike-in 500 ng of non-human DNA in 0.0001 pg of human DNA sample and submit it for sequencing on a HiSeq X Ten. The obvious reason is cheaper sequencing of non-human spike-in DNA.
But it still only runs WGS. Any bets on when the application menu opens up?
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