| Table of Contents |
|---|
http://loving.corral.tacc.utexas.edu/bioiteam/ which links to $BI/web
...
- General introduction (SPHS)
- Getting started at TACC
- Introduction to mapping
- Using the Integrative Genomics Viewer (IGV) (JB)
- start diploid mapping
Enrichment modules (4:30-5:00)
- Installing virtual machines OR samtools tricks OR data formats for UCSC genome browser (DP)
- Linux tutorial (SPHS)
Extras
- RunningUnix Running Unix & Perl for Biologiststutorial Biologists tutorial at TACC
Day 2: Calling Genome Variants
- Introduction to variant calling (SAMtools) (SPHS - expand to diploid, cover GATK pipeline; annovar seqanswer)
- Assess mapped data (VCF? BAM?) at UCSC genome browser (AW)
- Annotating variants (SPHS/DA)
- Download presentation on Advanced Genome Variant Calling|^Barrick_AdvancedGenomeVariantCalling_2012.pdf||||||||||\
Enrichment module (4:30-5:00)
- Installing Linux tools (JB/)
- Shell Scripting (SPHS/AB)
- Maybe start tophat via script (DA)
...
- SRA toolkit, UCSC Genome Browser
- Mapped read data evaluation (SAMtools) (SPHS)
- Calling variants in diploid genomes
- Variant calling with GATK
- Genome variation in mixed samples (FreeBayes, deepSNV)
- Identifying structural variants (SVDetect)
- Practical advice - short read re-sequencing data
Day 3: RNA-seq
- Intro materials - (SPHS - JB/DA)
- Differential gene expression analysis (JB - bedtools & R)
- Intro materials - splicing (SPHS - JB/DA)
- Differential expression with splice variant analysis (DA - tophat suite - mention genome ref bundles)
- 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)
- Maybe show how to run tophat here instead of end of day 2?
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