Question: Illumina R1 vs. R2 read quality differences - reasons?
1
gravatar for Anand Rao
24 months ago by
Anand Rao240
United States
Anand Rao240 wrote:

I am trying to understand the theoretical bases and practical causes for why R2 is poorer quality compared to R1 for Illumina Paired End sequencing.

While there are some posts here that discuss this observation: MiSeq: R1 vs. R2 reads show big quality difference - is that normal? Should I trim both R1 and R2 if only R2's quality is poor?

what I am most interested is in understanding WHY this happens. Could someone point me in the right direction please - specific papers, or an Illumina technical note, a Youtube presentation, etc. - anything useful. THANK YOU!

pe read quality illumina • 2.0k views
ADD COMMENTlink modified 24 months ago by Istvan Albert ♦♦ 81k • written 24 months ago by Anand Rao240
3
gravatar for Istvan Albert
24 months ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

The Illumina paired end sequencing involves a temporal separation and a mechanistic process.

The "first in pairs" are sequenced first then the fragments "bend" over, reattach, then reads in the second pair are sequenced on the same flow cell surface.

Depending on the protocol this second step may occur days later. Hence it is not unexpected to have lower qualities on read 2.

ADD COMMENTlink modified 24 months ago • written 24 months ago by Istvan Albert ♦♦ 81k
2
gravatar for genomax
24 months ago by
genomax71k
United States
genomax71k wrote:

See this thread on SA and my answer there.

ADD COMMENTlink modified 24 months ago • written 24 months ago by genomax71k
1

Thanks genomax

ADD REPLYlink written 24 months ago by Anand Rao240
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