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Old 03-17-2015, 01:16 PM   #1
scrosby
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Default HiSeq 3000/4000 2x150 data

Hello wise ones,

Has anyone out there had any paired-end long read experience. We'd love to see the run data (Q30 graphs, etc).

S
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Old 03-17-2015, 10:32 PM   #2
luc
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I do not believe there are any 3000's/4000s out there in the wild yet.
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Old 03-17-2015, 11:21 PM   #3
Brian Bushnell
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I would not expect any useful data from "Q30 graphs"; my understanding is that Illumina is currently planning mandatory Q-score quantization on the new platforms, as they do on NextSeq, which will render the quality scores mostly useless.
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Old 03-18-2015, 04:03 AM   #4
GenoMax
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There are some examples of HiSeq 4000 data in public area on BaseSpace. Don't know if they are long read since the description does not say anything specific.
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Old 03-18-2015, 05:11 AM   #5
scrosby
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Checked BaseSpace already. Just 2x76.
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Old 03-30-2015, 01:21 PM   #6
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We just received our HiSeq 4000 today and it will be a couple more months until we can get validation runs going.
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Old 05-08-2015, 05:02 AM   #7
Genohub
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Would you be open to listing your HiSeq 4000 on Genohub.com? There are many researchers hoping to get access. Are access to flow cells still a limiting factor?
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Old 05-08-2015, 05:13 AM   #8
GenoMax
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@scrosby: UC Davis lab had posted some 3000 data. http://seqanswers.com/forums/showthread.php?t=58353
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Old 06-04-2015, 01:37 AM   #9
QazSeDc
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As I believe many companies are still undergoing 4000 validation testing, but so far the graphs on 4000 raw data that i have seen are all pretty nice and stable beside the duplication problem everyone has already mentioned.
And by the way I think Q20 is enough to determine the quality of the sequence in most cases.

Last edited by QazSeDc; 06-04-2015 at 01:39 AM.
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Old 06-04-2015, 07:01 AM   #10
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Increased number of duplicate reads, preferential amplification of small fragments and shorter sequencing libraries?

Is this worth 900K?
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Old 06-04-2015, 10:29 AM   #11
Brian Bushnell
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Quote:
Originally Posted by QazSeDc View Post
And by the way I think Q20 is enough to determine the quality of the sequence in most cases.
...no, absolutely not. That's like determining the flavor of a bottle of wine by reading the label.

Quote:
Originally Posted by NextGenSeq
Increased number of duplicate reads, preferential amplification of small fragments and shorter sequencing libraries?

Is this worth 900K?
Not to me; I'd prefer the 2500, except when you need immense volume of short-insert overlapping fragments. For example, a time-and-space-series deep metagenome, or when sequencing a country's population...
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