Question: Why Does The Base Quality Drop Towards The End For Illumina Reads ?
4
gravatar for jack
4.9 years ago by
jack410
jack410 wrote:

Does anybody knows why, why base quality drops towards the end for Illumina reads ?

bioinformatics illumina • 7.5k views
ADD COMMENTlink modified 2.8 years ago by andrew.j.skelton735.4k • written 4.9 years ago by jack410
1

Good question - I have always accepted the phenomenon without really understanding the cause.

ADD REPLYlink written 4.9 years ago by Ian5.3k
11
gravatar for Istvan Albert
4.9 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

The illumina platform uses a so called sequencing by synthesis process. Bases are added one at a time and the consensus is determined in a cluster of identical sequences.

The source of errors can be numerous, here is one review that discusses the issues in more detail:

The challenges of sequencing by synthesis, Nature Biotech, 2009

In a nuthsell a short answer to the best of my understanding is this: Not all sequences in a cluster will grow at the same rate, this will slowly lead to a desynchronization as the errors accumulate. This is why the quality dips towards the end.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Istvan Albert ♦♦ 78k
1
gravatar for Vijay Lakhujani
2.8 years ago by
Vijay Lakhujani3.4k
India
Vijay Lakhujani3.4k wrote:

See this post:

Why does base quality of reads generally decreases at the end of the read? 

ADD COMMENTlink written 2.8 years ago by Vijay Lakhujani3.4k
0
gravatar for andrew.j.skelton73
2.8 years ago by
London
andrew.j.skelton735.4k wrote:

I'd highly recommend you check out this - The site as a whole is useful for explaining common things you'd see in sequencing, like primer bias. 

ADD COMMENTlink written 2.8 years ago by andrew.j.skelton735.4k

Link looks broken, can you check?

ADD REPLYlink written 2.8 years ago by Vijay Lakhujani3.4k

Seems to be down at the moment

ADD REPLYlink written 2.8 years ago by andrew.j.skelton735.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1062 users visited in the last hour