How To Install rna-star on Ubuntu 18.04
Introduction
In this tutorial we learn how to install rna-star on Ubuntu 18.04.
What is rna-star
rna-star is:
Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, the authors experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy.
There are three methods to install rna-star on Ubuntu 18.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install rna-star Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install rna-star using apt-get by running the following command:
sudo apt-get -y install rna-star
Install rna-star Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install rna-star using apt by running the following command:
sudo apt -y install rna-star
Install rna-star 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 rna-star using aptitude by running the following command:
sudo aptitude -y install rna-star
How To Uninstall rna-star on Ubuntu 18.04
To uninstall only the rna-star package we can use the following command:
sudo apt-get remove rna-star
Uninstall rna-star And Its Dependencies
To uninstall rna-star and its dependencies that are no longer needed by Ubuntu 18.04, we can use the command below:
sudo apt-get -y autoremove rna-star
Remove rna-star Configurations and Data
To remove rna-star configuration and data from Ubuntu 18.04 we can use the following command:
sudo apt-get -y purge rna-star
Remove rna-star configuration, data, and all of its dependencies
We can use the following command to remove rna-star configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge rna-star
References
Summary
In this tutorial we learn how to install rna-star package on Ubuntu 18.04 using different package management tools: apt, apt-get and aptitude.
