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A Data Carpentry Workshop

New Mexico State University

August 28-29, 2017

9:30 am - 5:00 pm

Instructors: Jason Williams


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 Data analysis and visualization in R and Cloud computing and command line for genomics. 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: 1780 E University Ave, Las Cruces, NM 88003. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Data Carpentry's Code of Conduct.

Contact: Please mail for more information.

Pre-Survey: Please take this pre-survey prior to the workshop.


Day 2: 9:30AM - 5:00PM

Morning: Using Linux to organize and process Genomics Data
Intro to the Linux Shell - Searching and Metadata
Project Organziation and Documentation
'For' loops - QC of Sequencing Data
Afternoon: Using Linux to Automate
Automating Analyses - Shell Scripting
Creating Workflows - Varient Calling Workflow
Workshop Conclusion Please take the post-survey

Post Workshop

How to Make This Work on Your Own
Launching Your Own Cloud Instances 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.