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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TransDecoder 5.5.0 detect coding regions

TransDecoder finds open reading frames in transcripts and predicts coding regions.This is the second step.

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 -> TransDecoder

Input File(s)

Use example_nt.fa from the directory above as test input.

You will also need the output folder of the 'TransDecoder 5.5.0 extract long ORFs' app.

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.

  • Use these parameters within the DE app interface:
    • in the 'options' section: choose 'dynamic' in the 'retain long ORFs mode field

Output File(s)

Expect these output files. For the test case, the output files you will find in the example_data directory are:

detect_coding_regions_output-- output directory from the 'predict coding regions' process

  • example_nt.fa.transdecoder.bed
  • example_nt.fa.transdecoder.cds
  • example_nt.fa.transdecoder.gff3
  • example_nt.fa.transdecoder.pep

The .pep file is a peptide FASTA file.

Tool Source for App

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