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.
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 |
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
- 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
- Tutorial - Start diploid mapping for Day 2
Enrichment modules (4:30-5:30)
- Sharing Linux tricks - linux one-liners (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)
Day 2: Calling Genome Variants
- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Introduction to genome variation
Introduction to variant calling presentation (JB)- Variant calling tutorial (SAMtools) (JB)
Enrichment module (12:30-1:30)
Enrichment modules (4:30-5:30)
- Shell Scripting (SPHS/AB)
Extras
- Calling variants in diploid genomes (SPHS)
- Variant calling with GATK (SPHS)
- Annotating variants (SPHS)
- Advanced genome variant calling presentation (JB)
- Visualize mapped data at UCSC genome browser (AB)
- Mapped read data evaluation (SAMtools) (SPHS, DP)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
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- SRA toolkit (AB)
Day 3: RNA-seq
- Integrative Genomics Viewer (IGV) tutorial (JB)
- Introduction to RNA-seq
- Differential gene expression analysis (JB)
- Differential expression with splice variant analysis
Enrichment module (12:30-1:30)
Possible Enrichment modules (4:30-5:30)
- Start tophat by submitting to lonestar (DA)
- Visualize mapped data at UCSC genome browser (AB)
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- Mapped read data evaluation (SAMtools) (SPHS, DP)
Extras
Day 4: Assembly and Annotation - Bacterial
Introduction to genome assembly- Genome Assembly Examples (SPHS)
- Tutorial: Genome Assembly (velvet) (SPHS)
- Genome Annotation (Glimmer3) (VR)
- Evaluating & Visualizing assemblies (bacterial)
Enrichment module (12:30-1:30)
Enrichment module (4:30-5:30)
- Transcriptome assembly & annotation
- Protein functional classification...
- Custom Genome Databases
Extras
- "I want to learn how to install and use this tool called ______ that we didn't talk about in class." (JB)