August 2012
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We will meet in Room 101B of the Flawn Academic Center (FAC) building. |
| Table of Contents |
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Your Instructors
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
SPHS | Director GSAF | Everything, if loosely defined (but especially | |
Jeff Barrick | 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 |
Geoff Colburn | GC | Barrick Lab | Mappers, variant callers |
Aaron Reba | AR | Barrick Lab | TACC, Python |
Vinicio Reynoso | VR | Barrick Lab | Genome assembly |
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Day 1: Linux/TACC Introduction and Read Mapping
- General introduction (SPHS)
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster (SPHS/AR)
- Introduction to next-gen sequencing technologies (SPHS)
- Application: Example genome variant calling pipeline (JB)
- Evaluating your raw sequencing data (JB/AB)
- Introduction to Mapping and Tutorial
(JB)- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Integrative Genomics Viewer (IGV) tutorial (Part 1) (JB)
- Tutorial - Start diploid mapping for Day 2
Enrichment modules (4:30-5:30)
- Sharing Linux tricks (SPHS)
- Making it easier to work on TACC from a Mac (JB)
Extras
- Running Unix & Perl for Biologists tutorial at TACC
- Installing Virtual machine & Linux on Windows (DP)
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Day 2: Calling Genome Variants
- Introduction to genome variation
- (JB)
- Variant calling tutorial (SAMtools) (JB)
- Integrative Genomics Viewer (IGV) tutorial (Part 2) (JB)
- (JB)
- Calling variants in diploid genomes (SPHS)
- Variant calling with GATK (SPHS)
- Visualize mapped data at UCSC genome browser (AB)
- Annotating variants (SPHS)
Enrichment module (12:30-1:30)
Enrichment modules (4:30-5:30)
- Shell Scripting (SPHS/AB)
Extras
- Mapped read data evaluation (SAMtools) (SPHS, DP)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- Practical advice - short read re-sequencing data
- SRA toolkit (AB)
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Day 3: RNA-seq
- Intro materials - (SPHS - JB/DA)
- Differential gene expression analysis (JB - bedtools & R)
- Differential expression with splice variant analysis
Enrichment module (12:30-1:30)
Enrichment module (4:30-5:30)
- Start tophat via script (DA)
Extras
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Day 4: Assembly and Annotation - Bacterial
- Genome Assembly (SPHS - add intro material)
- Genome Assembly (velvet) (SPHS)
- Genome Annotation (Glimmer3) (VR)
- Evaluating & Visualizing assemblies (bacterial)
Enrichment module (12:30-1:30)
- "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)
- Transcriptome assembly & annotation
- Protein functional classification...
- Custom Genome Databases