A Data Carpentry Workshop
The Jackson Laboratory
Sep 29-30, 2016
9:00 am - 5:00 pm
Instructors:
Sue McClatchy, Narayanan Raghupathy, Petr Simecek
Helpers:
Yuka Takemon, Dan Gatti
Sep 29-30, 2016
9:00 am - 5:00 pm
Instructors: Sue McClatchy, Narayanan Raghupathy, Petr Simecek
Helpers: Yuka Takemon, Dan Gatti
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.
We will cover Introduction to the Shell and Cloud Computing, The Shell and Project Setup, Know Your Data and Variant Calling and Workflow Automation. 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 workshop is open to researchers at all levels from the Jackson Laboratory and other institutions. We will create a supportive environment in which instructors assist with programming exercises and participants help one another. For this reason, on-site (rather than remote) participation is required.
Where: We'll be in the Breezeway Training Room in Bldg. 1, Unit 5 at the Jackson Laboratory, 600 Main Street, Bar Harbor, Maine. See this campus map for the location. Get directions with OpenStreetMap or Google Maps.
Requirements: Participants must bring a laptop with specific software installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.
Contact: Please mail susan.mcclatchy@jax.org for more information.
Preliminary Schedule
Thursday, September 29
| Morning | Introduction to the Shell and Cloud Computing |
| 09:00 | Workshop overview |
| 09:30 | Using cloud computing for genomics |
| 10:00 | Introduction to Unix: navigating, paths, shortcuts |
| 10:45 | Coffee/tea break |
| 11:00 | Introduction to Unix: examining files, modifying, writing |
| 12:00 | Lunch on your own |
| Afternoon | The Shell and Project Setup |
| 13:00 | Introduction to Unix: searching and redirection |
| 13:45 | Shell scripts |
| 14:30 | Coffee/tea break |
| 14:45 | Shell scripts (cont) |
| 15:45 | Genomics planning |
| 16:45 | Wrap-up |
Friday, September 30
| Morning | Know Your Data |
| 09:00 | Introduction to the workshop dataset |
| 09:15 | Examining data on the NCBI SRA database |
| 09:45 | QC of NGS data |
| 10:30 | Coffee/tea break |
| 10:45 | QC of NGS data (cont) |
| 12:00 | Lunch on your own |
| Afternoon | Variant Calling and Workflow Automation |
| 13:00 | Variant calling workflow (QC, alignment, variant calling) |
| 14:00 | Automating the workflow |
| 14:30 | Coffee/tea break |
| 14:45 | Automating the workflow (cont) |
| 16:45 | Wrap-up |
Etherpad: https://public.etherpad-mozilla.org/p/2016-09-29-jackson.
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 software named below. Please make sure to install everything 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.
Mac users
Windows users
- Putty Download putty.exe.
- Java
- Filezilla
- Integrative Genomics Viewer (IGV)
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.