TransDecoder

Owned by Simon Alexander
Last updated: Nov 17, 2022 by Declan Emmons (Unlicensed)
4 min read
1 Overview | 2 Setup and Install | 2.1 Step 01: Setup Perl | 2.2 Step 02: Setup TransDecoder: Download Source: | 3 Running the Application

Overview

TransDecoder (Find Coding Regions Within Transcripts): 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.

The latest releases can be found here.

Setup and Install

TransDecoder is a perl based application, that uses the additional URI::Escape module which must be installed before being able to run the application.

Step 01: Setup Perl

We will use the latest module version of perl available:

To see which versions are available, perform a module spider and check if a version has any dependencies:

[salexan5@tlog1 TransDecoder-TransDecoder-v5.5.0]$ module spider perl -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- perl: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Versions: perl/5.24.1 perl/5.26.2 perl/5.30.1 ... [salexan5@tlog1 TransDecoder-TransDecoder-v5.5.0]$ module spider perl/5.30.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- perl: perl/5.30.1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- You will need to load all module(s) on any one of the lines below before the "perl/5.30.1" module is available to load. swset/2018.05 gcc/7.3.0 swset/2018.05 intel/18.0.1 ...

 

Will load and use the latest ‘gcc’ version:

module load gcc/7.3.0 perl/5.30.1

 

Install the URI::Escape perl module:

Assuming this is the first time you’re installed a perl module, you will be prompted three times during the process:

Prompt 1: Type ‘yes’ and press Enter

Prompt2 [local::lib]]: Simply press Enter

Prompt3: Type ‘yes’ and press Enter

[] cpan URI::Escape Loading internal logger. Log::Log4perl recommended for better logging ... Would you like to configure as much as possible automatically? [yes] yes ... What approach do you want? (Choose 'local::lib', 'sudo' or 'manual') [local::lib] ... Would you like me to append that to /home/arcc-t01/.bashrc now? [yes] yes ... /bin/make install -- OK

 

Restart your session:

Since the above process has modified your .bashrc file, you need to restart your session for this changes to take affect:

[] exec bash

Alternatively, close and open a new session.

 

Step 02: Setup TransDecoder: Download Source:

Find the latest version from the release link above, and get the full URL to it. From a browser you can right click on a link and ‘Copy link address’ which can then be pasted into you session’s command line.

In this example, we are retrieving the .tar.gz file for version 5.5.0. Once downloaded we then unpack it.

[] wget https://github.com/TransDecoder/TransDecoder/archive/refs/tags/TransDecoder-v5.5.0.tar.gz [] tar -xvf TransDecoder-v5.5.0.tar.gz

We only have to do this once.

Running the Application

Note: You should not run this application directly on the login nodes, but either via an interactive session using salloc or submitted via sbatch. Please look on the ARCC Wiki for details on using these commands.

Every time you want to use the application, you will need to do the following:

# We want to use the same version of perl as we installed the URI::Escape module with [] module load gcc/7.3.0 perl/5.30.1 # Navigate to the folder where you uncompressed the source code. [] cd TransDecoder-TransDecoder-v5.5.0/ # Running the script you're interest in: # Running the script without any inputs will display the options available: [] ./TransDecoder.LongOrfs ######################################################################################## # ______ ___ __ # /_ __/______ ____ ___ / _ \___ _______ ___/ /__ ____ # / / / __/ _ `/ _\(_-</ // / -_) __/ _ \/ _ / -_) __/ # /_/ /_/ \_,_/_//_/___/____/\__/\__/\___/\_,_/\__/_/ .LongOrfs # ######################################################################################## # # Transdecoder.LongOrfs|http://transdecoder.github.io> - Transcriptome Protein Prediction # # # Required: # # -t <string> transcripts.fasta # # Optional: # # --gene_trans_map <string> gene-to-transcript identifier mapping file (tab-delimited, gene_id<tab>trans_id<return> ) # # -m <int> minimum protein length (default: 100) # # -G <string> genetic code (default: universal; see PerlDoc; options: Euplotes, Tetrahymena, Candida, Acetabularia) # # -S strand-specific (only analyzes top strand) # # --output_dir | -O <string> path to intended output directory (default: basename( -t val ) + ".transdecoder_dir") # # --genetic_code <string> Universal (default) # # Genetic Codes (derived from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi) # Acetabularia Candida Ciliate Dasycladacean Euplotid Hexamita Mesodinium Mitochondrial-Ascidian Mitochondrial-Chlorophycean Mitochondrial-Echinoderm Mitochondrial-Flatworm Mitochondrial-Invertebrates Mitochondrial-Protozoan Mitochondrial-Pterobranchia Mitochondrial-Scenedesmus_obliquus Mitochondrial-Thraustochytrium Mitochondrial-Trematode Mitochondrial-Vertebrates Mitochondrial-Yeast Pachysolen_tannophilus Peritrich SR1_Gracilibacteria Tetrahymena Universal # # # --version show version tag (5.5.0) # #########################################################################################