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Old 01-03-2011, 11:40 PM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 150
Arrow How to differentiate between PCR duplicates and real data?

Hi,

After IMHO intensive search in the internet for help, I must admit that i couldn't find anything too helpful, so I would like to ask here if there is a reasonable explanation or method to do that.

I am working with mRNA-Seq from Drosophila and after running the fastqc software got a very high duplication level.
I explaind it more specifically here (http://seqanswers.com/forums/showthr...1804#post31804), But as I think that it is an important question (at least for me), I would like to ask it separately again here.
It will be nice to get some data from both sides of the analysis. If someone has data of PCR duplications he/she can give, I would like to have a look at it.

Was it expected to have something like that in a RNA-Seq experiment?

How can someone reliably differentiate between the two cases?

Thanks for the help

Assa
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