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Can GAIIx introduce a bias in coverage A on T?

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  • Can GAIIx introduce a bias in coverage A on T?

    I have a graphic that show an increase in coverge of A over T, and It increses until the end sequence, in all lanes of paired ends runs of 72 pb. Can GAIIx introduce a bias in coverage A on T?
    Last edited by vjimenez; 05-12-2011, 06:55 AM.
    Veronica Jimenez Jacinto
    UUSM.

  • #2
    Originally posted by vjimenez View Post
    I have a graphic that show an increase in coverge of A over T, and It increses until the end sequence, in all lanes of paired ends runs of 72 pb. Can GAIIx introduce a bias in coverage A on T?
    Yes, for some reason, our recent datasets seem to favour A over T and G over C, when the quality is a bit crappy. We see a rise in N calls roughly correlating this discrepancy.

    An older dataset (of lower quality) of our is different, with C considerably over G, and T slightly over A.

    I don't know if this is an effect from the base-caller or if it's from the adapter sequences, but it's there, around 1% difference. How much of a gap are you seeing?
    Last edited by tonybolger; 05-18-2011, 04:09 AM.

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    • #3
      The gap between A and T is between 1% to 4% at the end of the sequence. But always in genomic apliaciones of eukaryotes.
      Veronica Jimenez Jacinto
      UUSM.

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      • #4
        Originally posted by vjimenez View Post
        The gap between A and T is between 1% to 4% at the end of the sequence. But always in genomic apliaciones of eukaryotes.
        Probably nothing too serious - how's the quality at that end?

        I guess if you're only seeing it in genomic data, it could be related to the specific adapters used.

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