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Old 04-02-2015, 06:48 AM   #1
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Default 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.
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Old 04-02-2015, 08:17 AM   #2
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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 (

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.
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Old 04-03-2015, 04:05 AM   #3
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Hi Genomax,
Thank you for the description above and sharing the pdf.

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


Last edited by bio_informatics; 04-03-2015 at 04:10 AM.
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fastqc, illumina, paired end

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