August 2012
Your Instructors
Name |
Initials |
Affiliation |
Expertise |
|---|---|---|---|
Scott Hunicke-Smith |
SPHS |
Director GSAF |
Everything, if loosely defined (but especially |
Jeff Barrick |
JB |
Asst. Prof. Biochemistry |
Microbes, Perl, Mac |
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, Python, Samtools |
Geoff Colburn |
GC |
Barrick Lab |
Mappers, variant callers |
Aaron Reba |
AR |
Barrick Lab |
TACC, Python |
Vinicio Reynoso |
VR |
Barrick Lab |
Genome assembly |
Day 1: Linux/TACC Introduction and Read Mapping
- General introduction (SPHS)
- Getting started at TACC
- 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)
- start diploid mapping (copy from Day 2 content)
Enrichment modules (4:30-5:30)
- Installing Linux virtual machine on Windows (DP)
- Sharing Linux tricks (SPHS)
- Making it easier to work on TACC from a Mac (JB)
Extras
Day 2: Calling Genome Variants
- Introduction to genome variation
- (JB)
- Variant calling tutorial (SAMtools) (JB)
- Integrative Genomics Viewer (IGV) tutorial (Part 2) (JB)
- (JB)
- Visualize mapped data at UCSC genome browser (AB)
- Calling variants in diploid genomes (SPHS)
- Variant calling with GATK (SPHS)
- Annotating variants (SPHS)
Enrichment module (12:30-1:30)
Enrichment modules (4:30-5:30)
- samtools tricks (DP)
- Shell Scripting (SPHS/AB)
Extras
- Mapped read data evaluation (SAMtools) (SPHS)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- Practical advice - short read re-sequencing data
- SRA toolkit, more UCSC Genome Browser (AB)
Day 3: RNA-seq
- Intro materials - (SPHS - JB/DA)
- Differential gene expression analysis (JB - bedtools & R)
- Differential expression with splice variant analysis
- MvA, volcano, heat maps, maybe goseq (R), cumberbund - check R version (SPHS/DA)
Enrichment module (12:30-1:30)
Enrichment module (4:30-5:30)
- Start tophat via script (DA)
Extras
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