Workshop Description

This course provides an introduction to high-throughput sequencing technology. The techniques taught in this workshop cover the more “universal” aspects of high-throughput sequence analysis from experimental design to sequencing methods and alignment methods. This course also will provide the student with an understanding of common file formats for sequence data and some of the limitations of sequencing techniques.

The hands-on portion of this course will be done using the Hoffman2 cluster and will involve programs designed to analyze read data and clean artifact and low-quality sequence as well as align the short reads to a reference genome.

By the end of the workshop, students will have an understanding of what high-throughput sequencing involves at the early steps before application-specific processes are utilized. Students will also have an understanding of the logic behind how many of these steps work. An optional unit for the last 30 minutes of this workshop will cover the logic behind aligner function in some depth.

Students who are comfortable working on the command line will find this course significantly easier than those who are inexperienced in this kind of environment. While Workshop 1 is not an absolute requirement, it is highly recommended for any student who is not already experienced working in a command line environment. A student who takes this workshop at the same time as Workshop 1 should not find any problems with timing of material between these two classes.

Day 1

The first day of the course covers the concepts of designing a sequencing study and planning how to analyze the results as well as understanding the available resources. This day is entirely lecture in order to allow any students with difficulties accessing the Hoffman2 cluster to get those issues fixed.

Slides for day 1 – 3 are located here.

Day 2

The second day of this course covers how to read raw sequence data as well as how to run a program to analyze the quality of the sequence and clean up any undesired/low quality sequence from the data.

Slides for day 1 – 3 are located here.

Day 3

The third day will cover how to align raw read data as well as how to understand the file format used to store read alignment data.

Slides for day 1 – 3 are located here.

Technical Requirements

Attendees are required to have Hoffman2 account prior to the start of class. To apply for an account, click here.

We have 10 brand new mac computers with all relevant sotware installed. If you would prefer to use your own laptop you may do so if you have the following installed PRIOR to class:

Instructor

Michael Weinstein was born in Los Angeles and grew up in Los Angeles and outside Washington D.C. He earned a B.S. in Microbiology, Immunology, and Molecular Genetics at UCLA in 2005 and a Ph.D. in Human Genetics in 2011. He is currently a postdoctoral researcher in the laboratory of Dr. Daniel H. Cohn studying the genetic causes and molecular biology of skeletal dysplasias. His primary wet-lab research is focused on understanding and modeling the pathology of skeletal disorders caused by dominant mutations in TRPV4 including autosomal-dominant brachyolmia, spondylometaphyseal dysplasia Kozlowski-type (SMDK), and metatropic dysplasia. His primary informatics project is finding new genetic variants causing brachyolmia (short spine) and brachyolmia-like disorders. While his current project is focused on developmental pathology and genetics, he also has extensive experience studying cardiovascular and metabolic disease as well as experience in cancer biology and infectious disease. One of his focuses with the Collaboratory is teaching computer programming and developing new applications to make exome and other biological analysis easier and more efficient (these programs can often be found at his github). When not working on these projects, he can often be found studying Filipino martial arts at the Wooden Center.

Email: michael.weinstein@ucla.edu
Education: B.Sc. Microbiology, Immunology, and Molecular Genetics UCLA 2005; Ph.D. Human Genetics UCLA 2011
Webpage: http://www.github.com/michael-weinstein

Workshop Details

Prerequisite: Unix*
Length: 3 days, 3hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28
*highly recommended, but not required.

Spring Dates

Oct. 3 – 5, 9:30 – 12:30pm