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You are here: Home / BioFrontiers Workshops / Previous BioFrontiers Workshops / Short-read 2015 / Day 3: Moving Files, Intro to Clusters, and Keeping Notes

Day 3: Moving Files, Intro to Clusters, and Keeping Notes

Welcome to Day 3 of the Short-Read Sequencing Analysis Workshop.The videos for day 3 will introduce you to the cluster we use (Vieques). You will learn how to move files to and from the cluster with SCP, as well as how to get data from NCBI or other source by ftp. We will also teach you how to use the text editor Emacs and how to submit jobs on the cluster using Torque. After day 3 you should have the skills necessary to work on Vieques to perform the sequencing analysis that is necessary for the rest of the class.

Day 3 Videos

Video1: Moving files to the cluster This video will introduce you to the Vieques server and show you how to move files from your local machine to Vieques using SCP 

Video2: Data transfer by ftp This video will show you how to transfer data from NCBI to your local machine and then transfer to Vieques

Video3: Working on Vieques In this video we will convert the .sra file from NCBI to the fastq format using the SRA Toolkit on Vieques. You will also be introduced to writing bash scripts

Video4: Introduction to text editors In this video you will be introduced to the text editor Emacs. 

Video5: Vieques (cluster) structure This video will explain the structure of Vieques and how to use Torque to submit jobs

Video6 Modules tutorials This short video will explain modules and how to load them in to Vieques

Day 3 Files

Day3 In-class slides

Day3 Homework

Day3 Homework solutions 

Additional Resources

Emacs cheat sheet We recommend that you print this out and bring it to class with you for the rest of the workshop

nano cheat sheet This is another editor that can be easy to use

Organizing Computational Projects This PLOS Computational Biology paper from 2009 is a great guide to organizing computational data for projects and how to keep a lab notebook on computational work 

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