Question: High Duplication Rate of Mapped In RNA-seq
3
gravatar for SeqNewbie
4.7 years ago by
SeqNewbie30
China
SeqNewbie30 wrote:

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 • 4.5k views
ADD COMMENTlink modified 4.7 years ago by Devon Ryan90k • written 4.7 years ago by SeqNewbie30
2
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

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 COMMENTlink written 4.7 years ago by Devon Ryan90k

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

ADD REPLYlink written 4.7 years ago by SeqNewbie30

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 REPLYlink written 4.7 years ago by Devon Ryan90k

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 REPLYlink written 4.7 years ago by SeqNewbie30

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 REPLYlink written 4.7 years ago by Michele Busby2.0k
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