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Day 1: Linux/TACC Introduction and Read Mapping
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- General introduction (SPHS)
- Linux refresher (SPHS)
- Using TACC's Lonestar Cluster (SPHS/AR)
- Introduction to next-gen sequencing technologies (SPHS)
- Application: Example genome variant calling pipeline (JB)
- Evaluating your raw sequencing data (JB/AB)
- Introduction to Mapping and Tutorial
(JB)- Mapping tutorial (bowtie2, BWA) (JB/GC)
- Integrative Genomics Viewer (IGV) tutorial (Part 1) (JB)
- Tutorial - Start diploid mapping for Day 2
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- Running Unix & Perl for Biologists tutorial at TACC
- Installing Virtual machine & Linux on Windows (DP)
Day 2: Calling Genome Variants
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- Introduction to genome variation
- (JB)
- Variant calling tutorial (SAMtools) (JB)
- Integrative Genomics Viewer (IGV) tutorial (Part 2) (JB)
- (JB)
- Calling variants in diploid genomes (SPHS)
- Variant calling with GATK (SPHS)
- Visualize mapped data at UCSC genome browser (AB)
- Annotating variants (SPHS)
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- Mapped read data evaluation (SAMtools) (SPHS)
- Samtools tricks (DP)
- Genome variation in mixed samples (FreeBayes, deepSNV) (JB)
- Identifying structural variants (SVDetect) (JB)
- Practical advice - short read re-sequencing data
- SRA toolkit, more UCSC Genome Browser (AB)
Day 3: RNA-seq
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- 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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Extras
Day 4: Assembly and Annotation - Bacterial
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- Genome Assembly (SPHS - add intro material)
- Genome Assembly (velvet) (SPHS)
- Genome Annotation (Glimmer3) (VR)
- Evaluating & Visualizing assemblies (bacterial)
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