RNA seq library preparation, PCR cycles

Question

[gaby_santos]

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 ?

[Asaf]

Yes, you might detect PCR bias as DE genes.

[gaby_santos]

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?

[Floris Brenk]

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...