How To Install tophat-recondition on Ubuntu 22.04
Introduction
In this tutorial we learn how to install tophat-recondition
on Ubuntu 22.04.
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 Ubuntu 22.04. We can use apt-get
, apt
and aptitude
. In the following sections we will describe each method. You can choose one of them.
Install 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 Ubuntu. 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 Ubuntu 22.04
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 Ubuntu 22.04, 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 Ubuntu 22.04 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
References
Summary
In this tutorial we learn how to install tophat-recondition
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.