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- samtools tricks (DP)
- Installing Linux tools (JB)
- Shell Scripting (SPHS/AB)
Extras
- SRA toolkit, more 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
- SRA toolkit, more UCSC Genome Browser
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)
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