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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This script conversts the juctions file producted by TopHat into GFF3 format for use with MAKER.


Quick Start



Test Data



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

Input File(s)

Use junctions.bed from the directory above as test input.

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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a tophat2gff3_results.gff as output. For the test case, the output file you will find in the example_data directory is named junctions.gff.

Tool Source for App




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