...
- Linux refresher
- Using TACC's Lonestar cluster
- Introduction to mapping (bowtie, BWA)
- Introduction to variant calling (SAMtools)
Extras
Day 2: Calling Genome Variants
- Using the Integrative Genomics Viewer (IGV)
- Shell Scripting
- Mapped read data evaluation (SAMtools)
- Installing Linux tools
- Identifying mutations in microbial genomes (breseq)Presentation on Advanced Genome Variant Calling
- Calling variants in diploid genomes
- Annotating variants —
Extras
- Genome variation in mixed samples (FreeBayes, deepSNV)
- SRA toolkit, UCSC Genome Browser
- Practical advice - short read re-sequencing data
- Variant calling with GATK
- Identifying structural variation
- Download presentation on Advanced Genome Variant Calling
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?)
...