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2016 Short-Read Sequencing Analysis Workshop

2016 Short-Read Sequencing Analysis Workshop

Here you will find the course materials for the 2016 Short-Read Sequencing Analysis Workshop. This workshop is run as a reverse classroom, we have 3-5 short video lectures that should be viewed before class each day. Time in the classroom is spent with discussion and hands-on learning. Each attendee will be running the programs during class time, and then will be expected to do homework on their own time outside of class to help solidify the skills they have learned.

The 2016 Workshop is being run on the BioFrontiers Vieques compute cluster. Each attendee will learn how to log on to the cluster and submit jobs to run the various analysis packages and programs.


Before you come

We have put together a page with important information for how to prepare for the workshop. Please make sure to review this page and download and install the programs you are going to need. 

We will have office hours on Monday, June 6 in JSCBB room B331 from 9-11am for attendees to come in and check that they can log into Vieques. Please stop by if you can, it will save a significant amount of time during class that day.


Workshop schedule and syllabus

2016 Workshop Schedule

2016 Workshop Syllabus


Daily Videos and Materials

Day 1, Introduction to Short-Read Sequencing (Monday, 6/6/16)

Day 2, Introduction to Linux (Tuesday, 6/7/16)

Day 3, Cluster Usage and Data Transfer (Wednesday, 6/8/16)

Day 4, Sequencing QC (Thursday, 6/9/16)

**Friday, 6/10/16 is a Skills Assessment day

Day 5, Introduction to Read Mapping and Visualization (Monday, 6/13/16)

Day 6, DNA Resequencing and Variant Calling (Tuesday, 6/14/16)

Day 7, ChIP-Seq Analysis (Wednesday, 6/15/16)

Day 8, RNA-Seq Day 1 (Thursday, 6/16/16)

Day 9, RNA-Seq Day 2 (Friday, 6/17/16)

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