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  • No usable signal found, it is possible clustering has failed

    My most recent MiSeq (Nano v2) run failed with the following error: No usable signal found, it is possible clustering has failed.
    I had a look at the focus images and there are clusters (see attached images). Cluster density is low, but comparable to previous runs that have finished without errors. Any idea what could be the problem?
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  • #2
    Hello miseq_user

    How diverse is the library and is there PhiX in the run? Is the cluster density comparable to previous runs on the MiSeq? Is there a chance you're comparing cluster densities on patterned v nonpatterned flow cells?

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    • #3
      Hello miseq_user
      Apart from gregrds answer, please also look into the following parameters
      1. NaOH used for denaturation. Whether it was freshly prepared and pH was above 12.5.
      2. Whether it is a metagenomics or any other type of library with low base diversity.
      3. Whether template line wash performed. If performed, whether enough washes were given after the template wash to remove residues of Sodium Hypochlorite.

      Hope this helps.

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