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  • FastQC output: Do I trim these?

    I am looking at the per base quality score of my RNA-Seq data, and found that the quality looks great. (as attached)

    But when I look at the per base sequence, the first 10 bases seems to be varying as if certain bases is preferred at certain positions. (as attached)

    Do I trim these off?
    Attached Files

  • #2
    That's likely caused by the "random" priming, in which case there's no need to trim it off (and doing so wouldn't improve anything anyway).

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