Question

High Duplication Rate of Mapped In RNA-seq

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10.2 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?

duplication RNA-Seq • 12k views

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by SeqNewbie ▴ 30

Ram · Answer 1 · 2014-09-15

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10.2 years ago

Devon Ryan 104k

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.

ADD COMMENT • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by Devon Ryan 104k

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

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by SeqNewbie ▴ 30

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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.

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by Devon Ryan 104k

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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.

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by SeqNewbie ▴ 30

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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?

ADD REPLY • link updated 2.9 years ago by Ram 44k • written 10.2 years ago by Michele Busby ★ 2.2k