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  • What does teh 51-mer count distribution plot in Preqc Output represent?

    Ignore the typo in the title please...

    I've been struggling to understand this plot. At first glance I thought it was telling me how many 51-mers there were in each genome, but a quick second look says this is not the case.

    From what I gather, it is showing how many times different 51-mers appear in the data, and what proportion of the total 51-mers they make up? But the proportions don't add up to 100%, at least they don't look like they do by just looking at the graph.

    Yes I have read the associated paper that first presented Preqc and what its output means (Exploring Genome Characteristics and Sequence
    Quality Without a Reference). Yes I have googled it. Yes I have read the short blurbs about the output posted here https://groups.google.com/forum/#!ms...U/oKoq54EZqKwJ

    I still don't understand. Could anyone explain it in very simple terms?

  • #2
    Without an image of the graph, I can't be sure, but typically these graphs plot number of unique kmers (Y) versus depth (X). So a point at X=12, Y=5000 would mean that there are 5000 kmers in the read data that each occur exactly 12 times.

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