PCR duplicates

[sequencingfan]

Hello,

what is PCR duplicate in NGS sequencing? Is there a detailed explanation of this problem? What is the impact of PCR duplictes to data analysis.

[jlei_face]

Here's a good link:

http://www.cureffi.org/2012/12/11/how-pcr-duplicates-arise-in-next-generation-sequencing/

[sequencingfan]

What about applications in which we use only Pcr to prepare libraries ( 16 s metagenomics,ion torrent ampliseq etc.).in my opinion most of reads for target region will start and end in the same positions.how to calculate real level of pcr duplication?

[Zaag]

What about applications in which we use only Pcr to prepare libraries ( 16 s metagenomics,ion torrent ampliseq etc.).in my opinion most of reads for target region will start and end in the same positions.how to calculate real level of pcr duplication?

If you are building an amplicon library you will only have PCR duplicates, so you leave them in. If you build a shotgun library you'll want to remove them.