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We have FFPE-tissues we would like to use for a sequencing run. we think we can get enough biological material, so the amount of RNA shouldn't be an issue, but we're not sure.

A unique molecular identifier (UMI) corrects for PCR bias resulting from multiple PCR cycles, but if I have enough material, I don't need to do too many cycles. On the other hand the library preparation protocol using UMI is more complicated and error-prone.

So, my general question is

Is it always recommended to use UMI in a sequencing run originating from FFPE-samples, regardless of the amount of the RNA that can be extracted?

Is there anything in the literature concerning this problem?

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  • $\begingroup$ I think you need to think about what you aim to gain out of the run? Expected outcomes alter how you should process the sample input. $\endgroup$
    – bob1
    Commented Jan 22 at 22:41

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