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Linux command line exercises for NGS data processing Linux command line exercises for NGS data processing by 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.

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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 $SHELL /bin/bash To see where you are in the file system: [uzi@quince-srv2 ~/linuxTutorial]$ pwd /home/uzi/linuxTutorial List the files in the current directory: [uzi@quince-srv2 ~/linuxTutorial]$ ls data Now try different commands from the sheet given below. Linux Commands Cheat Sheet • File System ls — list items in current directory ls -l — list items in current directory and show in long format to see perimissions, size, and modification date ls -a — list all items in current directory, including hidden files ls -F — list all items in current directory and show directories with a slash and executables with a star ls dir — list all items in directory dir cd dir — change directory to dir cd.