August 2012
Day 1: Linux/TACC Introduction and Read Mapping
- General introduction (SPHS)
- Getting started at TACC
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster
- Introduction to next-gen sequencing technologies
- Application: Example genome variant calling pipeline
- 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)
Extras
Day 2: Calling Genome Variants
- Introduction to genome variation
- (JB)
- Variant calling tutorial (SAMtools) (JB)
- Integrative Genomics Viewer (IGV) tutorial (Part 2) (JB)
- Visualize mapped data at UCSC genome browser (AB)
- (JB)
- Calling variants in diploid genomes
- Variant calling with GATK
- Annotating variants (SPHS/DA)
Enrichment modules (4:30-5:30)
- samtools tricks (DP)
- Installing Linux tools (JB)
- Shell Scripting (SPHS/AB)
Extras
- Mapped read data evaluation (SAMtools) (SPHS)
- Genome variation in mixed samples (FreeBayes, deepSNV)
- Identifying structural variants (SVDetect)
- Practical advice - short read re-sequencing data
- SRA toolkit, more UCSC Genome Browser
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 (4:30-5:30)
- Transcriptome assembly & annotation
- Protein functional classification...
- Custom Genome Databases