Transcript decoder 1.0
- de-confluence
- Roger Barthelson
Transcript decoder 1.0
Community rating: ?????
Finds open reading frames in transcripts and helps in their evaluation.
Quick Start
- To use Transcript decoder 1.0, import your RNA transcript contig data in fasta format.
- Resources:Â http://transdecoder.sourceforge.net/
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data ->Â Transcript_decoder
Input File(s)
Use testtranscripts.fasta 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 these parameters within the DE app interface:
- Minimum ORF size - 300
- genetic code - universal
- Minimum protein length - 50
Output File(s)
Expect a output files. For the test case, the output files you will find in the example_data directory are:
base_freqs.dat
 best_candidates.eclipsed_orfs_removed.bed
 best_candidates.eclipsed_orfs_removed.cds
 best_candidates.eclipsed_orfs_removed.gff3
 best_candidates.eclipsed_orfs_removed.pep
 best_candidates.gff3
 hexamer.scores
 longest_orfs.cds
 longest_orfs.cds.scores
 longest_orfs.cds.scores.selected
 longest_orfs.cds.top_500_longest
 longest_orfs.gff3
 longest_orfs.gff3.inx
 longest_orfs.pep
The most commonly used files will be the ones ending in .cds, which are the coding sequences of the transcript sequence contigs, and the .pep files, which are the translated peptide sequence files for the .cds files. The files that start with "longest_orfs" in their names are the open reading frame sequences that meet the criteria set when Transcript decoder was run, e.g. minimum ORF size 300 bp. The files that start with "best_candidates.eclipsed_orfs_removed" in their names are the longest_orfs files with redundant smaller sequences removed.