TransDecoder 5.5.0 detect coding regions
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
- To use TransDecoder 5.5.0 detect coding regions, import your RNA transcript contig data in fasta format; you will also need the output folder from the extract long ORFs app.
- Resources: https://github.com/TransDecoder/TransDecoder/wiki
Test Data
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.