How To Install transdecoder on Kali Linux

In this tutorial we learn how to install transdecoder on Kali Linux. transdecoder is find coding regions within RNA transcript sequences

Introduction

In this tutorial we learn how to install transdecoder on Kali Linux.

What is transdecoder

transdecoder is:

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

TransDecoder identifies likely coding sequences based on the following criteria:

  • a minimum length open reading frame (ORF) is found in a transcript sequence
  • a log-likelihood score similar to what is computed by the GeneID software is > 0.
  • the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
  • if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
  • optional the putative peptide has a match to a Pfam domain above the noise cutoff score.

There are three methods to install transdecoder on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install transdecoder Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install transdecoder using apt-get by running the following command:

sudo apt-get -y install transdecoder

Install transdecoder Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install transdecoder using apt by running the following command:

sudo apt -y install transdecoder

Install transdecoder Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install transdecoder using aptitude by running the following command:

sudo aptitude -y install transdecoder

How To Uninstall transdecoder on Kali Linux

To uninstall only the transdecoder package we can use the following command:

sudo apt-get remove transdecoder

Uninstall transdecoder And Its Dependencies

To uninstall transdecoder and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove transdecoder

Remove transdecoder Configurations and Data

To remove transdecoder configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge transdecoder

Remove transdecoder configuration, data, and all of its dependencies

We can use the following command to remove transdecoder configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge transdecoder

Dependencies

transdecoder have the following dependencies:

References

Summary

In this tutorial we learn how to install transdecoder package on Kali Linux using different package management tools: apt, apt-get and aptitude.