berkeley-express command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

berkeley-express: command not found

or when using sudo you get the following error message

sudo: berkeley-express: command not found

Solutions to berkeley-express: command not found

How To Fix berkeley-express: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu berkeley-express is provided by berkeley-express package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install berkeley-express

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install berkeley-express.

sudo apt -y install berkeley-express

Or if you have aptitude installed you can use the following command.

sudo aptitude install berkeley-express

Summary

In this tutorial we learn how to fix berkeley-express command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.