Question: High Sequence Duplication levels in FastQC
3
gravatar for EVR
4.4 years ago by
EVR570
Earth
EVR570 wrote:

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 

 

ADD COMMENTlink modified 4.4 years ago by Sam2.5k • written 4.4 years ago by EVR570
8
gravatar for Sam
4.4 years ago by
Sam2.5k
New York
Sam2.5k wrote:

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

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Sam2.5k
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