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  • Fastqc reports are different for forward and reverse strands?

    Hi All,
    I'm having Illumina, paired end reads for a bacterial genome. I'm newbie in NGS, paired end, etc terms.

    I ran fastqc on forward and reverse reads.

    My question:
    Why are reports different for R1 and R2?
    In my output, report [basic statistics plot] shows poor quality for R2 than R1. Is there any bias while sequencing?

    I know I'm putting a broad question and may sound lame.
    Bioinformaticscally calm

  • #2
    That is the sequencer's way of letting you know it got tired

    On a serious note, this "feature" has been part of illumina technology from early days. Clusters grow in size, phasing and other errors accumulate, reagents are sitting (though at 6-8C) in the instrument for a few days. These probably are all factors that contribute to some drop in Q-scores in read 2.

    In most cases the drop should not be large (http://www.illumina.com/documents/pr...e_Q-Scores.pdf).

    It is generally user samples (containing adapter dimers, small inserts, low nucleotide diversity to name a few) that ultimately lead to precipitous drops in Q-scores (the ones you are referring to) on read 2.

    Comment


    • #3
      Hi Genomax,
      Thank you for the description above and sharing the pdf.

      Yes, the difference isn't tremendous, Slight I'd say.

      Merci!
      Last edited by bio_informatics; 04-03-2015, 04:10 AM.
      Bioinformaticscally calm

      Comment

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