Fastq deduplication levels

Question

[shivangi.agarwal800]

Hi Guys,

I was checking the quality control parameters of a sample (DNA fastq ; paired end, sequenced on Illumina platform) using fastqc toolkit. I noticed that fastqc put a red cross on "Sequence Duplication Levels" panel, showing "percent of seqs remaining if deduplicated 35.06%". I have attached the graph here. Please have a look. Please help me to interpret it and do I need to remove the duplicated sequence ?

Thanks, Shivangi

Answer 1

[Istvan Albert]

The answer to the question is far more complicated than we assume, I tried twice to explain it

and I still don't quite remember what it really means - unless I re-read what I wrote

Revisiting the FastQC read duplication report

So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report

Answer 2

[GenoMax]

Please check this blog post from authors of FastQC: https://sequencing.qcfail.com/articles/libraries-can-contain-technical-duplication/

What is the intended application for your data? If the genome you are working with has a lot of repetitive sequence then this may be a perfectly normal result.