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  • FastQC warnings

    Hello,

    using FastQC I always get one error and two warnings for each of my samples (bacterial samples, WGS).

    Error:
    per base sequence conent
    --> here, I assume that tagmentation is the reason - so I can ignore this error warning. Someone told me that Illumina data usually fail here due to the fact that tagmentation is not as random as previously supposed

    Warnings (se figures)

    1. Sequence Length Distribution
    2. Sequence Duplication Levels

    Is this something to worry about? Why do I get warnings here?
    Attached Files

  • #2
    Sequence length distribution: it seems to be the result of trimming adapters

    Duplication Levels: deep sequencing in relation to library diversity

    per base sequence content: could be result of tagmentation but you have not posted this plot

    Comment


    • #3
      Neither of these warnings are worrisome.
      BTW, a 4 million base pair genome provides only 8 million possible places to start a sequence read. Any more reads that that and you will certainly have duplications.

      --
      Phillip

      Comment


      • #4
        Thank you for your answers!

        Comment

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