Transcript decoder 2.0
Transcript decoder 1.0
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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: 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 -> 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.