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- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Introduction to genome variation
(JB)- Variant calling tutorial (SAMtools) (JB)
- Integrative Genomics Viewer (IGV) tutorial (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)
Enrichment module (12:30-1:30)
Enrichment modules (4:30-5:30)
- Shell Scripting (SPHS/AB)
Extras
- 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)
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Day 3: RNA-seq
- Integrative Genomics Viewer (IGV) tutorial (JB)
- Differential gene expression analysis (JB - bedtools & R)
- Differential expression with splice variant analysis
...