Question: RNA seq library preparation, PCR cycles
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gravatar for gaby_santos
3.7 years ago by
gaby_santos10
gaby_santos10 wrote:

If during the library preparation I make different PCR cycles will my differential expression analysis will be biased because of the samples with higher PCR cycles? Would it be noiser ?

rna-seq • 1.2k views
ADD COMMENTlink written 3.7 years ago by gaby_santos10

Yes, you might detect PCR bias as DE genes.

ADD REPLYlink written 3.7 years ago by Asaf8.4k

So then all the samples should have the same PCR cycles? But why they will be biased if during the differential expression analysis I normalized the samples?

ADD REPLYlink written 3.7 years ago by gaby_santos10

I depends a bit on your experimental design meaning do you have 5 cases and 5 controls and all controls have more PCR cycles then yes it might be an issue. So maybe elaborate a bit more about the project and planned analyses...

ADD REPLYlink written 3.7 years ago by Floris Brenk970
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