High Sequence Duplication levels in FastQC

Question

[EVR]

Hi,

I am new to NGS analysis. I have RNAseq samples generated from Illumina platform. When the samples loaded onto FastQC , I noticed that there is high percentage Sequence Duplication level (> 70%) for all samples but the per base sequence quality for all samples are really good. How should I approach with these data? Is this normal for Illumina samples? Any guidance would be highly appreciated.

Thanks in advance

Answer 1

[Sam]

For RNA Seq, it is normal to see a high percentage of sequence duplication level. That is because the inherit nature of the RNA Sequencing is to count the depth of coverage of each gene. If you have a high coverage gene, it is likely you will encounter duplication.

As for exome sequencing, you would prefer a uniform coverage, therefore duplication might be a problem

Edit: Actually someone else has asked a similar question before High Duplication Rate of Mapped In RNA-seq