Alternatives to mirBase for mirDeep2 Input
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19 months ago
Jack ▴ 10

I am working on analyzing some high throughput data and trying to quantify which miRNAs are differentially expressed and by how much in my experiments. To do this I planned to use mirDeep2 and mirBase to acquire my precursors and mature miRNAs for my mirDeep2 input, but my model (Mustela putorius furo) is not yet annotated on mirBase. I found annotations for pre-miRNA and miRNA on RNAcentral, but its not immediately clear to me whether those are the hairpins and mature miRNAs I need for mirDeep2 to run. If anybody has any advice on using RNAcentral for mirDeep2 or other alternative databases that might include ferret sequences that would be greatly appreciated!

mirBase RNAcentral ferret RNAseq mirDeep2 • 496 views
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