How To Install stringtie on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 406 words
Introduction
In this tutorial we learn how to install stringtie on Ubuntu.
What is stringtie
stringtie is:
The abundance of transcripts in a human tissue sample can be determined by RNA sequencing. The exact sequence sampled may be random, depending on the technology used. And it may be short, i.e. shorter than the transcript. At some point, many shorter reads need to be assembled to the model the complete transcripts.
StringTie knows how to assemble of RNA-Seq into potential transcripts without the need of a reference genome and provides a quantification also of the splice variants.
There are three methods to install stringtie 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 stringtie Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install stringtie using apt-get by running the following command:
sudo apt-get -y install stringtie
Install stringtie Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install stringtie using apt by running the following command:
sudo apt -y install stringtie
Install stringtie 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 stringtie using aptitude by running the following command:
sudo aptitude -y install stringtie
How To Uninstall stringtie on Ubuntu
To uninstall only the stringtie package we can use the following command:
sudo apt-get remove stringtie
Uninstall stringtie And Its Dependencies
To uninstall stringtie and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove stringtie
Remove stringtie Configurations and Data
To remove stringtie configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge stringtie
Remove stringtie configuration, data, and all of its dependencies
We can use the following command to remove stringtie configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge stringtie
Dependencies
stringtie have the following dependencies:
References
Summary
In this tutorial we learn how to install stringtie package on Ubuntu using different package management tools: apt, apt-get and aptitude.