rapmap_pseudoindex command not found

Introduction

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

rapmap_pseudoindex: command not found

or when using sudo you get the following error message

sudo: rapmap_pseudoindex: command not found

Solutions to rapmap_pseudoindex: command not found

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

In Ubuntu rapmap_pseudoindex is provided by rapmap package.

rapmap is:

RapMap is a testing ground for ideas in quasi-mapping / (lightweight / pseudo) transcriptome alignment. That means that, at this point, it is somewhat experimental. The develop branch will have the latest improvements and additions, but is not guaranteed to be stable between commits. Breaking changes to the master branch will be accompanied by a tag to the version before the breaking change. Currently, RapMap is a stand-alone quasi-mapper that can be used with other tools. It is also being used as part of Sailfish and Salmon. Eventually, the hope is to create and stabilize an API so that it can be used as a library from other tools.

Quasi-mapping / (lightweight / pseudo)-alignment is the term that is used here for the type of information required for certain tasks (e.g. transcript quantification) that is less “heavyweight” than what is provided by traditional alignment. For example, one may only need to know the transcripts / contigs to which a read aligns and, perhaps, the position within those transcripts rather than the optimal alignment and base-for-base CIGAR string that aligns the read and substring of the transcript. For details on RapMap (quasi-mapping in particular), please check out the associated paper. Note: RapMap implements both quasi- mapping and pseudo-alignment (originally introduced in Bray et al. 2016), these two are not the same thing. They are distinct concepts, and RapMap simply happens to implement algorithms for computing both.

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

sudo apt-get -y install rapmap

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

You can also use apt command to install rapmap.

sudo apt -y install rapmap

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

sudo aptitude install rapmap

Summary

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