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.