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Preparing for the workshop

Preparing for the workshop

Here you will find some things we would like you to do before the beginning of the workshop.

For PC Users, please go to the Links for programs required for PC Users to download some programs you will need for the course, and watch the Server Access from Windows video for information on how to install and set up these programs.

For everyone attending the Summer 2015 course, we have set up some office hours with Cassidy and Jon in our IT group to help you get set up on the server. If at all possible please try to stop into JSCBB D222 between 9am-12pm on Monday to get set up. For PC users please have the programs downloaded and installed prior to coming in.

 Workshop Overview: 

This workshop is set up as a reverse classroom course. Attendees are to review a set of videos prior to the class each day, and then the majority of in-class time is spent working through examples and reviewing homework problems. For most days there will be some homework, but there will often be some class time in which to work through these. In order to get the most out of the workshop we ask that you come prepared each day, having watched the appropriate videos having worked on the homework problems. There is a lot of information to cover in 2 weeks, but being prepared each day will help you learn the most. We have added two "catch-up" days where you can make sure you understand the material covered so far and give people a chance to catch up if they have fallen behind. There will be a short quiz on the first catch-up day to make sure you have the skills that will be required for the next sections.

2015 Workshop Syllabus

Classroom sessions will be held in JSCBB A108 from 1-5pm each day of the class. 

Day 1, Monday June 8 - Course overview, Intro to Illumina, and Library QC (Jamie Kershner & Tim Read)

Day 2, Tuesday June 9 - Intro to Linux and editors (Joey Azofeifa & Joe Rokicki)

Day 3, Wednesday June 10 - Moving files, Intro to clusters, and Keeping notes (Joey Azofeifa & Daniel Malmer)

Day 4, Thursday June 11 - Read QC and Introduction to Mapping (Amber Sorenson & Daniel Malmer

Catch-up day, Friday June 12

Day 5, Monday June 15 - Read Mapping and Visualization (Jess Vera & Phil Richmond)

Day 6, Tuesday June 16 - Resequencing (Phil Richmond & Aaron Odell) - this is an optional class that will go over specific issues with genome resequencing including variant calling

Day 7, Wednesday June 17 - RNA-Seq and Differential Expression (Aaron Odell & Jess Vera) - this is an optional class that will go over specific issues related to RNA-seq analysis

Day 8, Thursday June 18 - Peak calling and ChIP-Seq (Amber Sorenson & Tim Read) - this is an optional class that will go over specific issues related to ChIP-seq and peak calling analysis

Catch-up day, Friday June 19