How To Install transdecoder on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 470 words
Introduction
In this tutorial we learn how to install transdecoder on Ubuntu.
What is transdecoder
transdecoder is:
TransDecoder 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.
TransDecoder identifies likely coding sequences based on the following criteria:
- a minimum length open reading frame (ORF) is found in a transcript sequence
- a log-likelihood score similar to what is computed by the GeneID software is > 0.
- the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
- if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
- optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
There are three methods to install transdecoder on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install transdecoder Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install transdecoder using apt-get by running the following command:
sudo apt-get -y install transdecoder
Install transdecoder Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install transdecoder using apt by running the following command:
sudo apt -y install transdecoder
Install transdecoder Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install transdecoder using aptitude by running the following command:
sudo aptitude -y install transdecoder
How To Uninstall transdecoder on Ubuntu
To uninstall only the transdecoder package we can use the following command:
sudo apt-get remove transdecoder
Uninstall transdecoder And Its Dependencies
To uninstall transdecoder and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove transdecoder
Remove transdecoder Configurations and Data
To remove transdecoder configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge transdecoder
Remove transdecoder configuration, data, and all of its dependencies
We can use the following command to remove transdecoder configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge transdecoder
Dependencies
transdecoder have the following dependencies:
References
Summary
In this tutorial we learn how to install transdecoder package on Ubuntu using different package management tools: apt, apt-get and aptitude.