Tutorial:Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
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Course materials available at https://wikis.utexas.edu/display/bioiteam/SSC+Intro+to+NGS+Bioinformatics+Course

Topics

  1. Linux/TACC Introduction and Read Mapping
    • Shell Scripting
    • Installing Linux tools
    • Introduction to mapping (bowtie, BWA)
    • Introduction to variant calling (SAMtools)
  2. Calling Genome Variants
    • Using the Integrative Genomics Viewer (IGV)
    • Mapped read data evaluation (SAMtools)
    • Identifying mutations in microbial genomes (breseq)
    • Calling variants in diploid genomes
    • Annotating variants
    • Variant calling with GATK
    • Genome variation in mixed samples (FreeBayes, deepSNV)
    • Identifying structural variants (SVDetect)
  3. RNA-seq
    • Differential gene expression analysis
    • Differential expression with splice variant analysis
    • Transcriptome assembly & annotation
  4. Assembly and Annotation
    • Genome Assembly
    • Genome Assembly (velvet)
    • Genome Annotation (Glimmer3)
    • Evaluating & Visualizing assemblies
    • SRA toolkit, UCSC Genome Browser
    • Custom Genome Databases
course training • 6.6k views
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