UCSF DSI genomic preprocessing

Welcome to the UCSF Data Science Initiative's genomic preprocessing workshop. We plan to show you how to preprocess raw sequencing data for the following analyses:

• DNA seq
• Bulk RNA seq
• scRNA seq

This repository is currently under development - materials are coming soon. For the curious ones out there: this class will be loosely based on Data Carpentry's genomics workshop.

Official UCSF DSI Course Materials

Team-reviewed, tested, and ready-to-use materials are coming soon - once available, the materials will always be hosted on our official UCSF Collaborative Learning Environment (CLE) genomic preprocessing workshop webpage.

Workshop Setup Instructions:

Please do not wait until the day of the workshop to do these installations! We cannot spend class time working through installation issues.

Installation instructions for this course are coming soon. If you have any questions about this repository, please email both Angelo and Karla:

• Angelo Pelonero: angelo.pelonero@ucsf.edu

• Karla Lindquist: karla.lindquist@ucsf.edu

Instructors will also be in the classroom half an hour before a workshop begins. However, this time will be for minor troubleshooting issues only. If you have major issues (or if you wait until this time to begin your installations) we cannot guarantee that you will be set up in time to follow along with the workshop.

GitHub and UCSF data security protocols:

Please be aware that GitHub is not certified for use with personal health information (PHI). Do not store or share any sensitive information via GitHub, even if kept in private repositories.

For more information regarding UCSF's security guidelines, please see the UCSF IRB guidelines for electronic data security.