How To Install transdecoder-doc on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 478 words
Introduction
In this tutorial we learn how to install transdecoder-doc on Ubuntu.
What is transdecoder-doc
transdecoder-doc 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.
This package contains the documentation and sample data.
There are three methods to install transdecoder-doc 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-doc 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-doc using apt-get by running the following command:
sudo apt-get -y install transdecoder-doc
Install transdecoder-doc Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install transdecoder-doc using apt by running the following command:
sudo apt -y install transdecoder-doc
Install transdecoder-doc 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-doc using aptitude by running the following command:
sudo aptitude -y install transdecoder-doc
How To Uninstall transdecoder-doc on Ubuntu
To uninstall only the transdecoder-doc package we can use the following command:
sudo apt-get remove transdecoder-doc
Uninstall transdecoder-doc And Its Dependencies
To uninstall transdecoder-doc and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove transdecoder-doc
Remove transdecoder-doc Configurations and Data
To remove transdecoder-doc configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge transdecoder-doc
Remove transdecoder-doc configuration, data, and all of its dependencies
We can use the following command to remove transdecoder-doc configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge transdecoder-doc
Dependencies
transdecoder-doc have the following dependencies:
References
Summary
In this tutorial we learn how to install transdecoder-doc package on Ubuntu using different package management tools: apt, apt-get and aptitude.