9:00 am - 4:30 pm
Instructors: Jason Williams, Sheldon McKay, Matthew Aiello-Lammens
Helpers: Joslynn Lee, Laura Graham, Jonathan Borrelli
This Genomics Data Carpentry workshop is for learning how to manage and analyze genomic data. This hands-on workshop requires no prior computational experience and teaches basic concepts, skills and tools for working more effectively with genomic data.
We will cover data and project organization, using cloud computing and the command line, running bioinformatics pipelines at the command line, and data analysis and visualization with R. 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.
Contact: Please mail firstname.lastname@example.org for more information.
Fee: Fees will cover coffee/snacks. Waivers can be requested by contacting organizer.
|Intro, Data Processing, and Organization|
|Pre-Survey (only take if you did not complete the link sent via email)|
|Intro to Data Carpentry||Jason|
|Getting started with the data||Jason||Getting your project started||Jason|
|Command line exploration of the data (unix shell)||Sheldon|
|Quality Control of NGS Data||Jason|
|NGS Data analysis|
|Know your data||Jason|
|Automating a workflow with a shell script||Sheldon|
|Automating a variant calling workflow||Sheldon|
|data analysis and visualization with R|
|Data analysis and visualization with R||Matthew|
|Moving Your Data||Jason|
|Please complete the post-workshop Survey||Everyone|
|Launching cloud instances after the workshop|
Launching your own instance
Note: Start here if you are working on the lessons on your own
|On your own|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.