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  • #16
    I am afraid something has gone wrong with this run. Either specific index cycles failed (where you see the . ) or more likely (hate to say this) your libraries may have failed. Either scenario would make this data unusable.

    Are you sure the adapters you used were good and/or there was no issue with the run itself (either hardware or software related)? You could submit a ticket to Illumina tech support. You seem to have access to full run folder so they will help you diagnose the problem. Even if you don't have a maintenance contract the diagnosis should be covered under regular tech support.

    The file you attached above has an odd format that I have not seen before. Contact Illumina tech support and see what they have to say.
    Last edited by GenoMax; 04-02-2020, 11:06 AM.

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    • #17
      Originally posted by GenoMax View Post
      I am afraid something has gone wrong with this run. Either specific index cycles failed (where you see the . ) or more likely (hate to say this) your libraries may have failed. Either scenario would make this data unusable.

      Are you sure the adapters you used were good and/or there was no issue with the run itself (either hardware or software related)? You could submit a ticket to Illumina tech support. You seem to have access to full run folder so they will help you diagnose the problem. Even if you don't have a maintenance contract the diagnosis should be covered under regular tech support.

      The file you attached above has an odd format that I have not seen before. Contact Illumina tech support and see what they have to say.
      OK. I will do this and I hope I can find a solution. You can not imagine how much effort I have put to get this results.

      Thank you very much for your support and I really appreciate your time spent to answer my queries.

      Regards,

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      • #18
        Please come back and post when you hear from tech support. I am curious to see the outcome of this as well.

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        • #19
          Originally posted by GenoMax View Post
          Ah so your run was dual-indexed. I am puzzled as to why your reads don't have any index sequence in fastq headers.
          For MiSeq data, MiSeq Reporter and I think BaseSpace don't include the index sequence in the headers.
          Josh Kinman

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          • #20
            Originally posted by jdk787 View Post
            For MiSeq data, MiSeq Reporter and I think BaseSpace don't include the index sequence in the headers.
            I see. We don't use either. Thanks for that info.

            In any case the Demux file seems to be in a different format. Again may be due to use of MiSeq reporter/BaseSpace.

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