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I am looking to perform expression analysis of miRNAs with normal RNA-seq data lacking small RNA-seq data?

Which path should I choose for known miRNAs and unknown new miRNAs?

Data set: rna-seq data that analyzes the expression differences of a plant under stress.

Objective To assess known and new miRNAs.

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  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Aug 28 at 14:41
  • $\begingroup$ This looks a good question, outside my area. It may be helpful to provide further details of your study and data set and clarify what the known miRNAs represent. $\endgroup$
    – M__
    Aug 29 at 14:22
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    $\begingroup$ There is rna-seq data that analyzes the expression differences of a plant under stress. From this data I would like to learn the expression profiles of known and new miRNAs. $\endgroup$ Aug 29 at 16:43

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You are going to have to look up the library prep protocol used, and determine if it will capture miRNA. My guess is, in the course of most RNASeq preps, small products are removed as contamination, so you won't have any real miRNA left behind.

I believe you need to use a special library prep designed for miRNA to study them.

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