Difference between revisions of "TransDecoder"

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==Required Modules==
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==Environment Modules==
===Serial===
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
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===Parallel (OpenMP)===
 
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* {{#var:app}}
 
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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=Validation=
 
* Validated 4/5/2018
 

Revision as of 13:39, 13 June 2022

Description

transdecoder website  

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.

System Variables

  • HPC_TRANSDECODER_DIR - installation directory