Fastqc reports are different for forward and reverse strands?

[bio_informatics]

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.

[GenoMax]

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.

[bio_informatics]

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

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

Merci!