...
May
...
2013
...
| Warning |
|---|
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. |
| Table of Contents |
|---|
Your Instructors
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
SPHS | Director GSAF | Everything, if loosely defined (but especially | |
JB | Asst. Prof. Biochemistry | Microbes, Perl, Mac, miscellanea | |
Dhivya Arasappan | 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 |
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...
| Anchor | ||||
|---|---|---|---|---|
|
Day 1: Linux/TACC Introduction and Read Mapping
Part 1: Linux/TACC Introduction
- General introduction (SPHS)
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster (SPHS/AR)
Part 2: Read Mapping
- Introduction to next-gen sequencing technologies (SPHS)
- Introduction to Mapping and Tutorial**
(JB) - Mapping tutorial (bowtie2, BWA) (JB/GC)
- Tutorial - Start diploid mapping for Day 2
Enrichment modules (4:30-5:30)
...
...
...
...
...
...
...
- (SPHS)
...
- Making
...
- it
...
- easier
...
- to
...
- work
...
- on
...
- TACC
...
- from
...
- a
...
- Mac/PC
...
- -
...
- using
...
- your
...
- own
...
- computer
...
- (AB/everyone)
...
Extras
- Running Unix & Perl for Biologists tutorial at TACC
- Installing Virtual machine & Linux on Windows (DP)
| Anchor | ||||
|---|---|---|---|---|
|
Day 2: Examining Raw and Aligned sequences, and Calling Genome Variants
Part 1. Examining Raw and Aligned sequences
- Practical advice - short read re-sequencing data
- Integrative Genomics Viewer (IGV) tutorial (JB)
- Evaluating your raw sequencing data (JB/AB)
- Mapped read data evaluation (SAMtools) (SPHS, DP)
Part 2. Calling Genome Variants
- Introduction to genome variation
- (JB)
- Variant calling tutorial (SAMtools) (JB)
- Variant calling with GATK (SPHS)
Enrichment module (12:30-1:30)
...
...
...
...
- (JB)
...
Enrichment
...
modules
...
(4:30-5:30)
...
...
...
- (SPHS/AB)
...
Extras
- Calling variants in diploid genomes (SPHS)
- Annotating variants (SPHS)
- (JB)
- Visualize mapped data at UCSC genome browser (AB)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- SRA toolkit (AB)
| Anchor | ||||
|---|---|---|---|---|
|
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)
...
...
...
...
...
...
...
- (
...
- JB)
...
Enrichment modules (4:30-5:30)
...
Extras
| Anchor | ||||
|---|---|---|---|---|
|
Day 4: Assembly and Annotation
Part 1. Genome Assembly
Part 2. Assembly Annotation
- Genome Annotation (Glimmer3) (VR)
- Evaluating & Visualizing assemblies (bacterial)
Enrichment module (12:30-1:30)
...
Enrichment
...
module
...
(4:30-5:30)
...
...
...
...
...
- Protein
...
- functional
...
- classification...
...
...
...
Extras
- "I
...
- want
...
- to
...
- learn
...
- how
...
- to
...
- install
...
- and
...
- use
...
- this
...
- tool
...
- called
...
- _____
...
- _
...
- that
...
- we
...
- didn't
...
- talk
...
- about
...
- in
...
- class."
...
- (JB)
...
Resources
...
...
...
...
...