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[وفاء]

I'm doing RNA-seq with the nf-core pipeline and have the following worries about the samples:

I have 9 biopsy for one patient after treatment. So, should I treat the 9 samples as a technical replicate, a biological replicate, or an independent sample?

[Asaf]

Please change the title to include some more information.

[ATpoint]

The essential information is missing: What is the question you want to answer with this and which analysis is planned?

Answer 1

[Asaf]

If these are different biopsies then they should be considered as biological replicates. When running the pipeline you could just leave them as different samples, you'll have to deal with this when analyzing the results, depending on the statistical tests you'll execute.