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  • Realistic output for HiSeq 4000

    The official spec for PF Clusters on the HiSeq 3000/4000 is 270-312M per lane. It seems that it is pretty easy to exceed this specification but I would like to ask regular operators of a 3000/4000 what PF cluster counts do you reliably get per lane? Is there a difference depending on library type?

    Thanks.

  • #2
    It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.

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    • #3
      Originally posted by misterc View Post
      It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
      Agreed. Long insert libraries (library molecules longer than 550 bp) will reduce yields and quality scores.

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      • #4
        Yield is not an issue as long as libraries have the right insert sizes. Illumina guidance is around 75% PF clusters for a good run.

        There are optical duplicates but they appear to be randomly distributed when checked recently (n=1).

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        • #5
          We usually get 300-400 million passing filter per lane on a HiSeq3000. "Optical" duplicates are typically below 10%, except with weird library types. Often the higher the read yield the lower the "optical duplicate" rate.

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