TransDecoder
Description
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).
optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
Required Modules
Serial
- transdecoder
System Variables
- HPC_TRANSDECODER_DIR - installation directory
Validation
- Validated 4/5/2018