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?
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.
60% is common? I thought it a little high. I don't have much experience in NGS. thx
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.
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.
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?
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy