Quality Control of Illumina Data at the Command Line.pdf

Quality Control of Illumina Data at the Command Line Quick UNIX Introduction: UNIX is an operating system like OSX or Windows. The interface between you and the UNIX OS is called “the shell”. There are a few flavors of shell but the MSI standard is bash. The shell is what you see, your environment, when you open PuTTY or Terminal. UNIX acts like any other operating system and allows you to store and create files then use them during processes (e.g. running a program). Unlike OSX or Windows UNIX is not visual and has to be navigated using simple commands though the shell. A Note about remote computing: The goal of this tutorial is to introduce you to using MSI computational resources. This means you are going to use your computer to talk to other computers and tell those computers what to do. This also means that you have to make sure you know how to navigate a different computational environment (UNIX) and the data you need is somewhere MSI systems can access it (i.e. not on your personal computer). Brief Outline of MSI: Login Node: When you access MSI systems the login node is the first system that you connect to. The login node is only there to direct you to other MSI systems. Lab System: A group of computers that can be accessed using the isub command. This is an older system with less computational power behind it. /labs/pbs Itasca System: This is the newer, faster, fancier computer system. Your group will need to have SUs to use this system. SUs are free; Itasca is awesome; sign up for SUs! /resources/job-queues PBS queuing: PBS is a queuing program that takes care of reserving and ordering jobs to be run on the different systems. PBS takes special commands that allow you to ask for a specific amount of time and computational power. Once you submit your job (i.e. program) it will get in line (in the queue) and will run once room opens up. Storage: Each group is allotted some amount of storage the default amount is 100GB but