How To Install tophat-recondition on Debian 12
Introduction
In this tutorial we learn how to install tophat-recondition on Debian 12.
What is tophat-recondition
tophat-recondition is:
tophat-recondition is a post-processor for TopHat unmapped reads (contained in unmapped.bam), making them compatible with downstream tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It also works around bugs in TopHat:
- the “mate is unmapped” SAM flag is not set on any reads in the unmapped.bam file (TopHat issue #3)
- the mapped mate of an unmapped read can be absent from accepted_hits.bam, creating a mismatch between the file and the unmapped read’s flags (TopHat issue #16)
There are three methods to install tophat-recondition on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install tophat-recondition Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install tophat-recondition using apt-get by running the following command:
sudo apt-get -y install tophat-recondition
Install tophat-recondition Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install tophat-recondition using apt by running the following command:
sudo apt -y install tophat-recondition
Install tophat-recondition 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install tophat-recondition using aptitude by running the following command:
sudo aptitude -y install tophat-recondition
How To Uninstall tophat-recondition on Debian 12
To uninstall only the tophat-recondition package we can use the following command:
sudo apt-get remove tophat-recondition
Uninstall tophat-recondition And Its Dependencies
To uninstall tophat-recondition and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove tophat-recondition
Remove tophat-recondition Configurations and Data
To remove tophat-recondition configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge tophat-recondition
Remove tophat-recondition configuration, data, and all of its dependencies
We can use the following command to remove tophat-recondition configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge tophat-recondition
Dependencies
tophat-recondition have the following dependencies:
References
Summary
In this tutorial we learn how to install tophat-recondition package on Debian 12 using different package management tools: apt, apt-get and aptitude.
