Data Carpentry Workshop: Genomics Data
Amsterdam Science park
March 22-23, 2017
9.30 - 17.00
Instructors:
Mateusz Kuzak, Lex Nederbragt, Dennis Schmitz, Sam Nooij, Anita Schürch
Helpers:
Sergio Arredondo, Malbert Rogers, Willem Ligtenberg
March 22-23, 2017
9.30 - 17.00
Instructors: Mateusz Kuzak, Lex Nederbragt, Dennis Schmitz, Sam Nooij, Anita Schürch
Helpers: Sergio Arredondo, Malbert Rogers, Willem Ligtenberg
General Information
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. The focus of this workshop is on working with genomics data and data management and analysis for genomics research.
We will cover Intro, Data Processing, and Organization, Data Cleaning and Visualization in R - Intro to Linux , Using Linux to organize and process Genomics Data and Using Linux to Automate. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.
Who: The course is aimed at graduate students and other researchers.
Where:
Science Park 140, 1098 XG Amsterdam.
Get directions with
OpenStreetMap
or
Google Maps
or
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 with internet access capabilities. They should have a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.
Contact: Please mail a.c.schurch@umcutrecht.nl for more information.
Preliminary Schedule
Surveys
Please be sure to complete these surveys before and after the workshop.
Day 1
| 09:30 | Intro to Data Carpentry | LN |
| 09:45 | Intro to the Data Set | LN |
| 10:00 | Connecting to the Cloud | MK |
| 10:30 | R and R Studio Orientation | MK |
| 11:00 | Dataframes and Metadata | MK |
| 11:30 | Dataframes Continued | MK |
| 12:00 | Data Cleaning and Manipulation with dplyr | MK |
| 12:30 | Lunch break | |
| 13:00 | Data Cleaning and Manipulation with dplyr (cont'd) | MK |
| 14:30 | Plotting and visualization in R | MK |
| 15:30 | Intro to the Linux Shell - Filesystem and Navigation | AS |
Day 2
| 09:30 | Intro to the Linux Shell - Searching and Metadata | SN |
| 10:30 | Project Organization and Documentation | AS |
| 11:30 | 'For' loops - QC of Sequencing Data | DS |
| 12:30 | Lunch break | |
| 13:00 | Automating Analyses - Shell Scripting | LN |
| 14:00 | Creating Workflows - Variant Calling Workflow | LN |
| 15:30 | Data Importing and Uploading | AS |
| 16:00 | Intro to SURFsara HPC resources | Natalie |
| 16:30 | Wrap up |
Etherpad: http://pad.software-carpentry.org/2017-03-22-amsterdam.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Setup
To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.
Please follow these Setup Instructions.
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.