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miRNAs quantification using mirdeep2 tool

I have 4 miRNA vigna mungo files. I have to discover the novel genes of miRNAs. For this purpose I go through many papers, at last I decided to use mirdeep2 tool.for running this tool for my research,

  • a FASTA file with the reference genome
  • a FASTA file with the reference miRBase mature miRNAs for the vigna mungo species
  • a FASTA file with the reference miRBase mature miRNAs for related species
  • a FASTA file with the reference miRBase precursor miRNAs for the vigna mungo species
  • a FASTA file with the deep sequencing reads.

the above files are needed, where can I download the files?

or any other way is there for quantifying the novel genes of vigna mungo

differential-expression mirdeep2 mirna
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written by Ashok • Ashok

This question does not make complete sense. If you have your own data files why do you need deep sequencing reads?

Genome (can be downloaded using Download button) from: https://www.ncbi.nlm.nih.gov/datasets/taxonomy/3915/

No miRNA's appear to be present in miRBase or RNAcentral.org. So you may need to do most of the discovery yourself.

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written by GenoMax GenoMax

thank you for your reply

https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md

i saw this github tutorial for miRNA quantification using mirdeep2 tool.they mentioned the below preliminary files for further proceedings. i dont where i have to download.

a FASTA file with the reference miRBase mature miRNAs for the vigna mungo species, a FASTA file with the reference miRBase precursor miRNAs for the vigna mungo species.

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written by Ashok • Ashok

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