Difference between revisions of "TransDecoder"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 53: Line 53:
 
-->
 
-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Revision as of 21:29, 6 December 2019

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.

Required Modules

Serial

  • transdecoder

System Variables

  • HPC_TRANSDECODER_DIR - installation directory





Validation

  • Validated 4/5/2018