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 default 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 running on 1 core and 1GB of memory:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load transdecoder

TransDecoder.LongOrfs -t transcripts.fasta

References

• TransDecoder GitHub
• TransDecoder wiki