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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_vmem=1G
#$ -l h_rt=1:0:0
module load transdecoder
TransDecoder.LongOrfs -t transcripts.fasta