Question: diffrent between CNV and pcr duplicate
0
gravatar for askari.arezou94
3 months ago by
IRAN/AHVAZ
askari.arezou9410 wrote:

Hi guys, How can distinguish the difference between Copy Number Variation and PCR duplicate in sequencing out put???

sequencing assembly genome • 162 views
ADD COMMENTlink modified 5 weeks ago • written 3 months ago by askari.arezou9410

I think PCR duplicates are handled early on in pipelines, using tools such as Picard's MarkDuplicates. My knowledge on this matter is quite outdated though, so you should wait for others' inputs and/or do some searching on your own.

ADD REPLYlink written 5 weeks ago by RamRS30k

ok, tnx for your response.

ADD REPLYlink written 5 weeks ago by askari.arezou9410

great response thank you.

ADD REPLYlink written 5 weeks ago by askari.arezou9410
1
gravatar for d-cameron
5 weeks ago by
d-cameron2.2k
Australia
d-cameron2.2k wrote:

PCR duplicates are a result of a DNA fragment that was used to prepare the library has been sequenced multiple times.

CNVs are changes in the actual number of copies of a section of DNA in the cells being sequenced.

These are fundamentally different concepts. CNVs are identifed based on the aggregate coverage (and/or variant allele fraction) of the genome. PCR duplicate just affect one DNA fragment in the library. CNVs reflect underlying biology. PCR duplicates are technical artefacts of sequencing library preparations that use PCR amplification.

ADD COMMENTlink written 5 weeks ago by d-cameron2.2k

great response. thank you

ADD REPLYlink written 5 weeks ago by askari.arezou9410
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