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 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)
- 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)
Day 2: Calling Genome Variants
- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Introduction to genome variation
- (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)
- (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)
- Practical advice - short read re-sequencing data
- SRA toolkit (AB)
Day 3: RNA-seq
- Integrative Genomics Viewer (IGV) tutorial (JB)
- 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)
- Mapped read data evaluation (SAMtools) (SPHS, DP)
Extras
Day 4: Assembly and Annotation - Bacterial
- Genome Assembly Examples (SPHS)
- Tutorial: 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