Workshop Description

High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies.

We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short reads to a reference genome. At the end of this workshop, students will better understand the logic behind how many of these steps work.

Students who are comfortable working with the command line will find this course significantly easier than those who are inexperienced in command-line interface. 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 a Hoffman2 account. To apply for an account, click here. UCLA participants who lack a faculty sponsor and non-UCLA participants may apply for a temporary Hoffman2 account, requesting sponsorship from Collaboratory Workshops.
  • We strongly encourage attendees to bring a laptop capable of accessing UCLA’s WiFi.

Please have the following installed on your laptop PRIOR to class:

Instructor

Michael Weinstein, Ph.D., 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

Reviews

Michael is one of the best instructors I’ve had; he’s great at explaining complex concepts and is perfect for teaching this course.
Fall 2018 Student

Game changing!

Fall 2018 Student
I really enjoyed the course and the way Michael taught it, especially that he provided so many insider tips and shared links for further resources. Great learning experience and everything was well organized. Thank you so much.
Fall 2018 Student

Great course!! Initially challenging, but by the last day it felt good to be able to do so many tasks that on the first day I didn’t know how to do.

Fall 2018 Student

Workshop Details

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

Winter 2019 Dates

January 8, 9, and 10, 2019
9:00 AM – 12:00 PM