transit command not found

Introduction

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

transit: command not found

or when using sudo you get the following error message

sudo: transit: command not found

Solutions to transit: command not found

How To Fix transit: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu transit is provided by tnseq-transit package.

tnseq-transit is:

This is a software that can be used to analyze Tn-Seq datasets. It includes various statistical calculations of essentiality of genes or genomic regions (including conditional essentiality between 2 conditions). These methods were developed and tested as a collaboration between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)

TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1 or Tn5 datasets.

TRANSIT assumes you have already done pre-processing of raw sequencing files (.fastq) and extracted read counts into a .wig formatted file. The .wig file should contain the counts at all sites where an insertion could take place (including sites with no reads). For Himar1 datasets this is all TA sites in the genome. For Tn5 datasets this would be all nucleotides in the genome.

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

sudo apt-get -y install tnseq-transit

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

You can also use apt command to install tnseq-transit.

sudo apt -y install tnseq-transit

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

sudo aptitude install tnseq-transit

Summary

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