TransDecoder 5.5.0 extract long ORFs
TransDecoder 5.5.0 extract long ORFs
Finds open reading frames in transcripts.
Quick Start
- To use TransDecoder 5.5.0 extract long ORFs, 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.
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 default parameters.
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
The .pep file is a peptide FASTA file.