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- Using the Integrative Genomics Viewer (IGV)
- Shell Scripting
- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Identifying mutations in microbial genomes (breseq)
- Calling variants in diploid genomes
- Annotating variants
Extras
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Additional topics
- SRA toolkit, UCSC Genome BrowserPractical advice - short read re-sequencing data
- Variant calling with GATK
- Genome variation in mixed samples (FreeBayes, deepSNV)
- Identifying structural variation
Extras
- Download presentation on Advanced Genome Variant Calling
- Practical advice - short read re-sequencing data
Day 3: RNA-seq
- Differential gene expression analysis
- Splice variant analysis
<break> - non-coding RNA analysis annotation - unique mapping (shrimp/grep), miRNA’s abundance/editing, other: snoRNA, snRNA, lincRNA, piRNA, tRNA, degradome, etc. etc. (not poly-A; not annotated)
- Transcriptome assembly & annotation velvet/oases, TrinityRNAseq; BLAST, GOminer, (ELI?)
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