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  • 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

  • #2
    I do not believe there are any 3000's/4000s out there in the wild yet.

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    • #3
      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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      • #4
        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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        • #5
          Checked BaseSpace already. Just 2x76.

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          • #6
            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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            • #7
              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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              • #8
                @scrosby: UC Davis lab had posted some 3000 data. http://seqanswers.com/forums/showthread.php?t=58353

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                • #9
                  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, 12:39 AM.

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                  • #10
                    Increased number of duplicate reads, preferential amplification of small fragments and shorter sequencing libraries?

                    Is this worth 900K?

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                    • #11
                      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.

                      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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