High Duplication Rate of Mapped In RNA-seq

Question

[SeqNewbie]

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?

Answer 1

[Devon Ryan]

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.

[SeqNewbie]

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

[Devon Ryan]

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.

[SeqNewbie]

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.

[Michele Busby]

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?