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.
License
For more information see https://github.com/TransDecoder/TransDecoder/blob/master/LICENSE.txt
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of transdecoder and load default version of transdecoder as
module avail transdecoder/ # list available modules module load transdecoder # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail transdecoder
and choose explicit version you want to use.
Documentation
http://transdecoder.github.io/