The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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miRDeep2 2.0.0.8

 

 

This app identifies known and novel miRNAs in deep sequencing data.

Quick Start

  • To use miRDeep2 2.0.0.8,  provide a fasta file of sequencing reads, fasta file of the reference genome and a miRDeep2 arf file of those reads mapped to that genome. 
    • Optionally, one can also provide known miRNAs and precursors from this species or a closely related one. These will likely improve the output but they are not required. 
  • Resources: https://github.com/rajewsky-lab/mirdeep2/tree/master/tutorial_dir

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> miRDeep2

Input File(s)

reads_collapsed.fa

cel.fa

reads_collapsed_vs_genome.arf

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below. 

Check all 3 boxes at the bottom of the input section to indicate that you are not providing known miRNAs or precursors.

Leave all parameters as default.

Output File(s)

For the test case, the output file you will find in the example_data directory is result_25_07_2018_t_16_23_07.csv


Tool Source for App

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