Question: Normalization for RNA-Seq samples
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gravatar for  DataFanatic
3 days ago by
DataFanatic260
DataFanatic260 wrote:

Hi I want to extract genes that are expressed in a tissue-specific manner, not expressed, expressed across tissues. I am working with RNA-Seq data across different tissues.

I’m sure others have done this experiment already. I have the following questions:

  1. I will start with a counts table, output of featureCounts, how would I normalize samples, usually I would use DESeq2, but in this case, I am not using DESeq2. (I will have data generated in different batches, labs, library size, technical variation.)

  2. What is an appropriate threshold for expressed vs. non-expressed, and can this information be derived accurately from RNA-seq data.

I hope this makes sense. Best!

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