Introduction
In this tutorial we learn how to install bitseq on Ubuntu 20.04.
What is bitseq
bitseq is:
BitSeq is an application for inferring expression levels of individual
transcripts from sequencing (RNA-Seq) data and estimating differential
expression (DE) between conditions. An advantage of this approach is the
ability to account for both technical uncertainty and intrinsic biological
variance in order to avoid false DE calls. The technical contribution to the
uncertainty comes both from finite read-depth and the possibly ambiguous
mapping of reads to multiple transcripts.
There are three methods to install bitseq on Ubuntu 20.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install bitseq Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install bitseq using apt-get by running the following command:
sudo apt-get -y install bitseq
Install bitseq Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install bitseq using apt by running the following command:
sudo apt -y install bitseq
Install bitseq 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 bitseq using aptitude by running the following command:
sudo aptitude -y install bitseq
How To Uninstall bitseq on Ubuntu 20.04
To uninstall only the bitseq package we can use the following command:
sudo apt-get remove bitseq
Uninstall bitseq And Its Dependencies
To uninstall bitseq and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove bitseq
Remove bitseq Configurations and Data
To remove bitseq configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge bitseq
Remove bitseq configuration, data, and all of its dependencies
We can use the following command to remove bitseq configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bitseq
References
Summary
In this tutorial we learn how to install bitseq package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.
