Child pages
  • SSC Intro to NGS Bioinformatics Course
Skip to end of metadata
Go to start of metadata

May 2013

We will meet in Room 101B of the Flawn Academic Center (FAC) building.  We STRONGLY encourage you to use the computers provided in the classroom, but you may also bring your personal laptops.

Resources tool list, file formats & more

Link to Etherpad: https://etherpad.mozilla.org/g2NxIEAFWL

Use this to post any questions you have about the lessons and tutorials.

Your Instructors

Name

Initials

Affiliation

Expertise

Scott Hunicke-Smith

SPHS

Director GSAF

Everything, if loosely defined (but especially awk)

Jeff Barrick

JB

Asst. Prof. Biochemistry

Microbes, Perl, C++, Mac, miscellanea

Dhivya Arasappan (in absentia)

DA

GSAF

RNA-seq, transcriptome assembly

Anna Battenhouse

AB

Iyer Lab

Eukaryotes, Bash scripting, UCSC Genome Browser

Daechan Park

DP

Iyer Lab

Eukaryotes, ChIP-seq, Python, Samtools

Nichole Bennett

NB

Parmesan/Singer Labs

Python, R, Unix

Dan Deatherage

DD

Barrick Lab

Unix, Python, NGS Library Prep

Nathan Abell

NA

Iyer Lab

Eukaryotes, RNA-Seq

instructor action item list

 Info for the instructors

Day 1a: Scott 1b: Jeff
Day 2a: Jeff, Daechan, Anna, 2b: Scott
Day 3a: Jeff 3b: Iyer lab
Day 4a: Jeff, 4b: Scott

Instructors: meet 9am Monday for final check

Each Part 1/Part 2 section needs to be standardized with:
*Learning Objectives
*Theory
*Workflow diagram (data, toolbox/recipe, exercises)
*Tutorial (bulk of time here)
*Recap learning objectives
*Next steps...

Day 1: Linux/TACC Introduction and Read Mapping

Part 1: Linux/TACC Introduction

Part 2: Read Mapping

Enrichment modules (4:30-5:30)

Extras

Day 2: Handling Raw and Aligned sequences, and Calling Genome Variants

Part 1. Handling Raw and Aligned sequences

Part 2. Calling Genome Variants

Enrichment module (12:30-1:30)

Enrichment modules (4:30-5:30)

Extras

Day 3: RNA-seq

Part 1. Introduction to RNA-seq Counting

Part 2. The Tuxedo RNA-seq Pipeline (Tophat & Cufflinks)

Enrichment module (12:30-1:30)

Enrichment modules (4:30-5:30)

Extras

Day 4: Assembly and Annotation

Part 1. Genome Assembly

Part 2. Assembly Annotation

Enrichment module (12:30-1:30)

  • Office hours: "I want to learn how to install and use this tool called ______ that we didn't talk about in class." (JB).

Enrichment module (4:30-5:30)

Resources

As you're getting settled

  • No labels