<![CDATA[BOL: Linux command line exercises for NGS data processing]]> https://bioinformaticsonline.com/bookmarks/view/27967/linux-command-line-exercises-for-ngs-data-processing? https://bioinformaticsonline.com/bookmarks/view/27967/linux-command-line-exercises-for-ngs-data-processing Wed, 22 Jun 2016 07:59:39 -0500 https://bioinformaticsonline.com/bookmarks/view/27967/linux-command-line-exercises-for-ngs-data-processing <![CDATA[Linux command line exercises for NGS data processing]]> The purpose of this tutorial is to introduce students to the frequently used tools for NGS analysis as well as giving experience in writing one-liners. Copy the required files to your current directory, change directory (cd) to the linuxTutorial folder, and do all the processing inside:

[uzi@quince-srv2 ~/]$ cp -r /home/opt/MScBioinformatics/linuxTutorial .
[uzi@quince-srv2 ~/]$ cd linuxTutorial
[uzi@quince-srv2 ~/linuxTutorial]$

I have deliberately chosen Awk in the exercises as it is a language in itself and is used more often to manipulate NGS data as compared to the other command line tools such as grep, sed, perl etc. Furthermore, having a command on awk will make it easier to understand advanced tutorials such as Illumina Amplicons Processing Workflow.

In Linux, we use a shell that is a program that takes your commands from the keyboard and gives them to the operating system. Most Linux systems utilize Bourne Again SHell (bash), but there are several additional shell programs on a typical Linux system such as ksh, tcsh, and zsh. To see which shell you are using, type

[uzi@quince-srv2 ~/linuxTutorial]$ echo $SHELL

/bin/bash

Address of the bookmark: http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/linux.html

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