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  • Maximum insert size with Hiseq 3000

    What is the maximum size of insert allowed/optimum in Hiseq 3000? For one of our analysis, we needed a longer insert size (~800bp) which is ok in the case of 2000 but i was told that it is not good in the case of 3000. Can anyone comment on this?

  • #2
    Anything over 500 bp is not recommended.

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    • #3
      I heard fragments from 400bp on or even below would start causing problems?

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      • #4
        Please see:
        http://dnatech.genomecenter.ucdavis....data-download/

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        • #5
          If the size bias is so extreme, does it mean that applications with non-random insert sizes shouldn't be run on the HiSeq3000/4000 at all?

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          • #6
            This thread has some useful information about data characteristics from that HiSeq 3000 dataset linked above: http://seqanswers.com/forums/showthread.php?t=58353
            Last edited by GenoMax; 07-23-2015, 03:55 AM.

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            • #7
              Thanks for the link!

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