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.
Environment Modules¶
Run module spider transdecoder to find out what environment modules are available for this application.
Environment Variables¶
- HPC_TRANSDECODER_DIR - installation directory
- HPC_TRANSDECODER_DOC - documentation directory
Categories¶
biology, ngs