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 --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load transdecoder
TransDecoder.LongOrfs -t transcripts.fasta