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  • Does analysis of DE genes with Trinity need replicates?

    I'd like to use Trinity to analyze DG genes of a non-model animal. According to the protocol for reference generation and analysis with Trinity on Nat Protoc. 2013, it seems that the analysis didn't use replicates, just used paired end reads for each treatment. Do my understanding is right?

    Greatly appreciate any answer for it !!

  • #2
    Originally posted by wmseq View Post
    I'd like to use Trinity to analyze DG genes of a non-model animal. According to the protocol for reference generation and analysis with Trinity on Nat Protoc. 2013, it seems that the analysis didn't use replicates, just used paired end reads for each treatment. Do my understanding is right?
    You may do Differential Expression without replicates, and Trinity provides scripts for such case. However, you should not do so, if possible, because you will have low power and inflated false positives. Check this paper (Liu et al. Bioinformatics. 2014; 30:301-304) for some background.

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    • #3
      nepossiver,

      Thank you very much for your advice!!!

      Then, could I follow the protocol and analyze the DE genes with replicates?

      Comment

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