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 mapper

 

This app maps sequencing reads to a Bowtie-indexed genome and produces a mapping file in arf format for use with other miRDeep2 apps. 

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 

cel.1.ebwt

cel.2.ebwt

cel.3.ebwt

cel.4.ebwt

cel.rev.1.ebwt

cel.rev.2.ebwt

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.

Select FASTA as the reads input file format and provide 'cel' as the genome index file prefix. 

Leave all other parameters as default.

Provide output file names. 

Output File(s)

Expect a file named exactly as you name it as output. For the test case, the output files you will find in the example_data directory are mapper_processed_out and mapped_out

Tool Source for App

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