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- Installing Linux virtual machine on Windows (DP)
- Sharing Linux tricks (SPHS)
- Making it easier to work on TACC from a Mac (JB+)
Extras
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- 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)
- (JB)
- Calling variants in diploid genomes (SPHS)
- Variant calling with GATK (SPHS)
- Annotating variants (SPHS)
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- Mapped read data evaluation (SAMtools) (SPHS)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect)
- Practical advice - short read re-sequencing data (JB)
- 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)
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Enrichment module (4:30-5:30)
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