What it does

TransDecoder identifies candidate coding regions within transcript sequences such as those generated by de novo RNA-Seq transcript assembly using Trinity or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

TransDecoder identifies likely coding sequences based on the following criteria:

• a minimum length open reading frame (ORF) is found in a transcript sequence.
• a log-likelihood score similar to what is computed by the GeneID software is > 0.
• the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
• if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
• a PSSM is built/trained/used to refine the start codon prediction.
• optional the putative peptide has a match to a Pfam domain above the noise cutoff score.

Step 1: Extract long open reading frames

By default, TransDecoder.LongOrfs will identify ORFs that are at least 100 amino acids long. You can lower this via the '-m' parameter, but know that the rate of false positive ORF predictions increases drastically with shorter minimum length criteria.

Step 2: (optional and not part of this wrapper)

The result "longest ORFs (PEP)" can be used to identify ORFs with homology to known proteins via BlastP or Pfam searches (details).

Step 3: Predict the likely coding regions

Optionally apply results of homology searches in this step and re-run the whole analysis.

Input

• FASTA file with transcripts
• (optional) gene-to-transcript identifier mapping file
• (optional) BLAST or Pfam database file (details)

Output

LongOrfs

• longest ORFs (PEP/FASTA): all ORFs meeting the minimum length criteria, regardless of coding potential
• longest ORFs (GFF3): positions of all ORFs as found in the target transcripts
• longest ORFs (CDS/FASTA): the nucleotide coding sequence for all detected ORFs

Predict

• Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed
• Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs
• Results (GFF3): positions within the target transcripts of the final selected ORFs
• Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV
• Plots: sequence logos and scores (compressed PDF)

Other

• Log file

References

More information are available on GitHub.