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 quantifier

 

 

This app maps deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. 

Quick Start

Test Data

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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.fasta 

mature_ref_this_species.fa

precursors_ref_this_species.fa

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. 

Leave all parameters as default.

Output File(s)

For the test case, the output file you will find in the example_data directory is miRNAs_expressed_all_samples_1532534506.csv

Tool Source for App

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