Question: Do I need to mark duplicates for sequencing data using multiplex PCR to prepare library?
0
gravatar for MatthewP
16 months ago by
MatthewP290
China
MatthewP290 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 • 414 views
ADD COMMENTlink modified 16 months ago by finswimmer12k • written 16 months ago by MatthewP290
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 16 months ago by ATpoint25k
2
gravatar for finswimmer
16 months ago by
finswimmer12k
Germany
finswimmer12k wrote:

Hello,

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

fin swimmer

ADD COMMENTlink written 16 months ago by finswimmer12k
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