Data Carpentry Workshop: Introduction to Reproducible Genomics @ TU Delft, EWI room: LB 01.010

June 4-5 2019

9:00-17:00

Instructors: Raúl Ortiz Merino, Marcel van den Broek, Santosh Ilamparuthi, Esther Plomp

Helpers: Mario Beck, Nicolas Dintzer, Barbara Vreede, Kees den Heijer

General Information

This is a Data Carpentry Workshop, with a special focus on sequence handling for variant calling using the cloud resources, the workshop will introduce you to Genomic concepts and scripting. For those unfamiliar with the concept, Data Carpentry aims at systematically delivering workshops on the fundamental data skills needed to conduct research. What you will learn during the workshop will largely influence the way in which you handle data in a fully independent way, free from proprietary software and storage platforms. The contents of this workshop will be the Genomics Curriculum. Check what to expect if you’re attending a workshop. For more details about what will be covered please see the schedule below.

Who: This workshop is open for researchers associated to the Faculty of Applied Sciences and the Faculty of Electrical Engineering, Mathematics & Computer Science @TU Delft. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

What: We will start with an introduction to the command line and use of command line utilities to analyze sequence quality and perform variant calling. All using publicly available datasets and connecting to and using cloud computing.

Where: Mekelweg 4, 2628 CD Delft. Get directions with OpenStreetMap or Google Maps.

When: June 4-5 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email P.M.MartinezLavanchy@tudelft.nl for more information.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1 - June 4th

Before starting Make sure you have filled in the Pre-workshop survey
Morning Project organization for genomics
MorningCloud Genomics
AfternoonShell for genomics
Evening END

Day 2 - June 5th

Morning Data wrangling and processing
Afternoon Data wrangling and processing continuation
Evening Make sure you have filled in the Post-workshop survey
END

Schedule

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

Project Organization

  • Data Tidiness
  • Planning for NGS Projects
  • Examining Data on the NCBI SRA Database
  • Reference

Introduction to Cloud Computing for Genomics

  • Why of cloud computing
  • Logging onto Cloud
  • Basic functions
  • Advanced Functions
  • Reference

Introduction to the Command Line for Genomics

  • Navigating Files and Directories
  • Redirection
  • Writing Shell Scripts
  • Reference

Data Wrangling and Processing for Genomics

  • Assessing Read Quality (FASTQ)
  • Trimming and Filtering
  • Variant Calling Workflow
  • Automating a Variant Calling Workflow
  • Reference

Setup

To participate in a Data Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

To participate in a Data Carpentry workshop, you will need working copies of the software described below. Please make sure to install everything and try opening it to make sure it works before the start of your workshop. If you run into any problems, please feel free to email the instructor or arrive early to your workshop on the first day. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.

Platform-specific Notes

This workshop will be using the software outlined in the install instructions below. Please see the section for your operating system for those directions.

Windows

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Windows should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. Putty

    3. You will need a terminal program to access the AWS Cloud/HPC cluster.
    • Go to the Putty download page
    • Click on putty.exe link to download the install file
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
  3. FTP Client (Filezilla)

    4. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect

Mac

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Mac should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect

Linux

Please go through all the installation steps below and make sure that you not only installed them, but start them up to make sure they're working. If you have any problems, don't hesitate to email the instructors to ask for help, or arrive early on the first day of the workshop to get help.

  1. A spreadsheet program

    2. For this workshop you will need a spreadsheet program. Many people already have Microsoft Excel installed, and if you do, you're set!
    If you need a spreadsheet program, there are a few other options, like OpenOffice and LibreOffice. Install instructions for LibreOffice, which is free and open source, are here.
    • Download the Installer
      Install LibreOffice by going to the installation page. The version for Linux should automatically be selected. Click Download Version 6.0.3 or later. You will go to a page that asks about a donation, but you don't need to make one. Your download should begin automatically.
    • Install LibreOffice
      Once the installer is downloaded, double click on it and it should install.
    • To use LibreOffice, double click on the icon and it will open.
  2. FTP Client (Filezilla)

    3. An FTP client will help you transfer files easily between your computer and the cloud.
    • Go to the Filezila download page
    • Chose the download link appropriate to your system
    • To use it, double-click on the downloaded file
    • Follow any installation instructions, if any
    • At the workshop we will give you additional information (e.g. host, username, port) to connect