High Duplication Rate of Mapped In RNA-seq
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7.1 years ago
SeqNewbie ▴ 30

Hi, I am doing RNA-seq. When i use RNA-SeQC to do the quality control, i found a large proportion of duplication reads. Duplication Rate of Mapped is about 60%. What should I do for this? Any influence on gene expression analysis?

RNA-Seq duplication • 7.1k views
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7.1 years ago

A high apparent duplication rate with RNAseq is to be expected (particularly if this is total RNA). This is generally not something to worry about.
 

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60% is common? I thought it a little high. I don't have much experience in NGS. thx

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Depending on the experiment type it's not too out there. Any experiment with a few really highly expressed genes will have metrics like this.

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ok,i am sequencing cancer cell lines. Most of my results are 50-60% duplication rate. Someone told me 1X100bp sequencing leads to a high rate of duplication.

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I think 60% could be pretty high, even for single end, depending on your sequencing depth and if it's mammalian.

I would check what % of your reads are aligning to rRNA.  If your rRNA removal failed that could be your problem. Otherwise, you might have a low complexity library.  Is it low input?   Do you have another library to compare it to?  

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