TransDecoder 5.5.0
TransDecoder 5.5.0
Finds open reading frames in transcripts and predicts coding regions. TransDecoder has two functions. This app runs both functions as a pipeline.
Quick Start
- To use TransDecoder 5.5.0, import your RNA transcript contig data in fasta format.
- 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 in BOTH the extract long ORFs and predict coding regions sections
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 'predict coding regions' '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:
example_nt.fa.transdecoder_dir--output directory from the 'extract long ORFs' process
- base_freqs.dat
- longest_orfs.cds
- longest_orfs.gff3
- longest_orfs.pep
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
In both cases the .pep file is a peptide FASTA file.