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Upon completion of the course, please take moment to provide your thoughts on the class. Your feedback is greatly appreciated and will be used to help improve future education initiatives!

[http://tinyurl.com/iihg-biocourse-feedback]

Bioinformatics Course "Cheat Sheet"

This file contains definitions and links to valuable tools and databases: Cheat Sheet

Agenda and slides for the IIHG Bioinformatics Short Course:

Day 1: Wednesday, August 1

Location

Time

Title (click to listen to recording)

Instructor

Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 am to 9:00 am

“The Magic of MPS” (1 hour)
*Recording contains first 3 Wed. Morning lectures conjoined

David Dimmock

Clinical Decision Making Based on Complete Genome Sequencing_Dimmock.pdf *Recording contains all Wed. Morning sessions conjoined

Kelch Conference Room 1289 CBRB

9:00 am to 9:30 am

Course Overview – Background, Goals for the Course, and Glossary of Terms (30 minutes)
*Recording contains first 3 Wed. Morning lectures conjoined

Eliot Shearer

IIHG-course-overview.pdf

Kelch Conference Room 1289 CBRB

9:30 am to 10:20 am

Next-Gen Sequencers Overview – Pros and Cons of each system; library preparation overview (50 minutes)
*Recording contains first 3 Wed. Morning lectures conjoined

Kevin Knudtson

Knudtson_GalaxyWorkshop_08012012.pdf

 

10:20 am to 10:40 am

Break 

 

 

Kelch Conference Room 1289 CBRB

10:40 am to 11:30 am

Experimental Design – The importance of filtering: inheritance models, segregation analysis, limitations and possibilities, etc. (50 minutes)

Richard Smith

The Importance of Filtering.pdf

Kelch Conference Room 1289 CBRB

11:30 am to 12:00 pm

Tour of the Genomics Core at the University of Iowa College of Medicine  (30 minutes)

Kevin Knudtson

 

EMRB Atrium

12:00 PM to 1:00 PM

Lunch


 

Hardin Information Commons

1:00 pm to 1:30 pm

Introduction to Data Analysis with MPS Data Sets (30 minutes)
*Recording contains into to lab session 1 as well

Ann Black

IIHG_Bioinformatics_Course.pdf

Hardin Information Commons

1:30 pm to 5:00 pm

Lab Session 1: Experimental Design for MPS Experiments – Using Galaxy to manipulate large data sets; creating a BED file for experimental design
*Recording contains into to Data Analysis and Lab 1 Intro

Lab instructors

Lab1_Instructions.pdf

Richard Smith’s home (11 Cherry Lane; 338-6404)

 6:00 PM to 8:00 PM

BBQ Dinner

 

 

Day 2: Thursday, August 2

Location

Time

Title (click to listen to recording)

Instructor

Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 AM to 9:00 AM

Quality Check / Quality Assessment of MPS Data, Sequence Capture Assessment (60 minutes)
*Recording contains first two Thursday morning lectures

Andre Altmann

Lecture_20120802_Altmann_MPS_QC.pdf

Kelch Conference Room 1289 CBRB

9:00 AM to 9:50 AM

Read Alignment Algorithms (50 minutes)
*Recording contains first two Thursday morning lectures

Tom Bair

IIHG_Bioinformatics_Course_alignment.pdf

 

9:50 AM to 10:10 AM

Break 

 

 

Kelch Conference Room 1289 CBRB

10:10 AM to 11:10 AM

Variant Calling Algorithms – SNVs and indels, in pooled and non-pooled data sets ( 1 hour)
*Recording contains last two Thursday morning lectures

Andre Altmann

Lecture_20120802_Altmann_MPS_SNPcall.pdf

Kelch Conference Room 1289 CBRB

11:10 AM to 12:10 PM

Detecting Copy Number Variants with MPS Data (1 hour)
*Recording contains last two Thursday morning lectures

Alex S. Nord

ASN_CNV_20120731.pdf

EMRB Atrium

12:10 PM to 1:00 PM

Lunch


 

Hardin Information Commons

1:00 PM to 5:00 PM

Lab Session 2: QC/QA of MPS data, Read Alignment, Variant Calling

Lab Instructors

Lab II-handout.pdf



Dinner on your own.

 

 

Day 3: Friday, August 3

Location

Time

Title (click to listen to recording)

Instructor

 Slides/Lab Instructions

Kelch Conference Room 1289 CBRB

8:00 AM to 9:00 AM

Data Annotation and Filtering Overview (1 hour)
*Recording contains first two Friday morning lectures

Alex S. Nord

ASN_Filtering_20120803.pdf

Kelch Conference Room 1289 CBRB

9:00 AM to 9:50 AM

Data management and data storage issues when dealing with NGS data sets (50 minutes)
*Recording contains first two Friday morning lectures

Ben Rogers

BioinformaticsShortCourseDataManagementAndStorage.pptx

 

9:50 AM to 10:10 AM

Break

 

 

Kelch Conference Room 1289 CBRB

10:10 AM to 10:40 AM

Practical considerations for grants and budgets (30 minutes)
*Recording contains last two Friday morning lectures

Ben Darbro

BioinformaticsCourseTalk.pdf

Kelch Conference Room 1289 CBRB

10:40 AM to 11:40 AM

Other Applications for MPS – RNASeq, Transcriptome, Methylome, etc. (1 hour)
*Recording contains first last Friday morning lectures

Tom Bair

IIHG_Bioinformatics_other_tech-1.pdf

EMRB Atrium

12:00 PM to 1:00 PM

Lunch


 

EMRB Atrium 

1:00 PM to 2:00 PM

Breakout Sessions with Course Instructors -- Q & A

 

 

Hardin Information Commons

2:00 PM to 5:00 PM

Lab Session 3: Annotating and Filtering Data Sets, Identifying Causal Variants, Exome Variant Data

Lab Instructors

LabSession3-overview.pdf
annotation-explanation.pdf
IIHG_Bioinformatics_Course-lab session3.pptx.pdf


5:00 PM

Course Adjourns

 

 

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