How To Install berkeley-express on Kali Linux

In this tutorial we learn how to install berkeley-express on Kali Linux. berkeley-express is Streaming quantification for high-throughput sequencing

Introduction

In this tutorial we learn how to install berkeley-express on Kali Linux.

What is berkeley-express

berkeley-express is:

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk.

In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias.

eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance.

There are three methods to install berkeley-express 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 berkeley-express Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install berkeley-express

Install berkeley-express Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install berkeley-express

Install berkeley-express 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 berkeley-express using aptitude by running the following command:

sudo aptitude -y install berkeley-express

How To Uninstall berkeley-express on Kali Linux

To uninstall only the berkeley-express package we can use the following command:

sudo apt-get remove berkeley-express

Uninstall berkeley-express And Its Dependencies

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

sudo apt-get -y autoremove berkeley-express

Remove berkeley-express Configurations and Data

To remove berkeley-express configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge berkeley-express

Remove berkeley-express configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge berkeley-express

Dependencies

berkeley-express have the following dependencies:

References

Summary

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