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TransDecoder

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

TransDecoder is available as a module on Apocrita.

Usage

To run the latest installed version of TransDecoder, simply load the transdecoder module:

 $ module load transdecoder
 $ TransDecoder.LongOrfs -t <fasta_file>
 $ TransDecoder.Predict -t <fasta_file>

For full usage documentation, run TransDecoder.LongOrfs -h or TransDecoder.Predict -h

Example job

Serial job

Here is an example job using 1 core and 1GB of memory:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_vmem=1G
#$ -l h_rt=1:0:0

module load transdecoder
TransDecoder.LongOrfs -t transcripts.fasta

References