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