Question: Do I need to mark duplicates for sequencing data using multiplex PCR to prepare library?
0
gravatar for MatthewP
23 months ago by
MatthewP620
China
MatthewP620 wrote:

Hello. I have some mtDNA sequencing data using multiplex PCR to prepare library, which means using many primers to 'copy' whole mtDNA from whole genome DNA by PCR, then use those fragments to perform sequencing. I used fastp to filtered my raw data, and the result shows:

Filtering result:
reads passed filter: 340702
reads failed due to low quality: 19374
reads failed due to too many N: 68
reads failed due to too short: 38
reads with adapter trimmed: 11738
bases trimmed due to adapters: 687212

Duplication rate: 96.892%

It has extremely high duplication rate, I think this may caused by library prepare for using multiplex PCR. My question is should I mark duplicates in such situation? Thanks everyone.

multiplex pcr picard mtdna • 522 views
ADD COMMENTlink modified 23 months ago by finswimmer13k • written 23 months ago by MatthewP620
1

What question do you want to answer? As the mitochondrial genome is only like 17kb, excessive duplication rate is normal and expected.

ADD REPLYlink written 23 months ago by ATpoint35k
2
gravatar for finswimmer
23 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Hello,

No, you shouldn't mark the duplicates. As by design all your reads are duplicates.

fin swimmer

ADD COMMENTlink written 23 months ago by finswimmer13k
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