Applied Computational Genomics Course at UU: Spring 2020

• Faculty: Aaron Quinlan (aquinlan at genetics.utah.edu)
• Teaching assistants: Michael Cormier (cormiermichaelj @ gmail.com), Katie Owings (katie.owings @ utah.edu), Ryan Miller (miller.ryan.h @ gmail.com), and Mark Wadsworth (mew225 @ gmail.com)
• Meets Tu and Th from 9:10-10:30 in EIHG Auditorium; January 7 - April 21
• TA Hours: Monday and Wednesday, 10-11am, HSEB

Overview

This course will provide a comprehensive introduction to fundamental concepts and experimental approaches in the analysis and interpretation of experimental genomics data. It will be structured as a series of lectures covering key concepts and analytical strategies. A diverse range of biological questions enabled by modern DNA sequencing technologies will be explored including sequence alignment, the identification of genetic variation, structural variation, and ChIP-seq and RNA-seq analysis. Students will learn and apply the fundamental data formats and analysis strategies that underlie computational genomics research. The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses.

Grading policy

All assignments are due on the date stated in class. Ten percent of the grade will be deducted for each 24 hours that the assignment is late.

Course lecture slides

• All slide decks (in Google Drive)
• Jan 7, 2020: Course overview and Intro to UNIX
• Jan 9, 2020: Intro to UNIX, Part 2
• Jan 14, 2020: The human genome
  • slides
  • youtube
• Jan 16, 2020: Pattern searching in the human genome
  • slides
  • youtube
• Jan 21, 2020: Genetic Variation
  • slides
  • youtube
• Jan 23, 2020: DNA sequencing technologies and FASTQ format
  • slides
  • youtube
• Jan 28, 2020: DNA sequence mapping and alignment
  • slides
  • youtube
• Jan 30, 2020: SAM/BAM format, samtools, and IGV
  • slides
  • youtube
• Feb 4, 2020: SNP and INDEL discovery (part 1)
  • slides
  • youtube
• Feb 6, 2020: SNP and INDEL discovery (part 2)
  • slides
  • youtube
• Feb 11, 2020: VCF format, Hardy Weinberg Equilibrium, VCF toolkits
  • slides
  • youtube
• Feb 18, 2020: VCF annotation and interpetation
• Feb 20, 2020: Structural and copy number variation
• Feb 20, 2020: Germline mutation
• Feb 25, 2020 (Who???): Genome Annotation and Resources
• Feb 27, 2020: Genome Annotation Formats. And awk.
• Mar 3, 2020: Genome arithmetic with bedtools
• Mar 5, 2020: Real world analyses with bedtools.
• Mar 17, 2020: RNA-seq analysis
• Mar 19, 2020: DESeq workshop
• Mar 24, 2020: Intro to Bash scripting
• Mar 26, 2020 (who???): Working with clusters, shell profiles, UNIX extras.
• Mar 31, 2020: Continuous distributions and descriptive statistics
• April 2, 2020: The Central Limit Theorem and Confidence Intervals
• April 7, 2020: The t-statistic, t-distribution, t-tests, and p-values
• April 14, 2020: Intro to regression (students watch video
• April 17, 2020: Group Presentations (1)
• April 21, 2020: Group Presentations (2)

Homework

• [Homework 1: Basic Unix analysis]
• [Homework 2: DNA Pattern exploration in a FASTA file]
• [Homework 3: Working with the FASTQ format]
• [Homework 4: BAM files, samtools, IGV]
• [Homework 5: Exploring genetic variation in VCF files]
• [Homework 6: Bedtools analysis problems. Bottom of page]

Syllabus

• Class 1 (Tu Jan 9; Layer): Course overview and Intro to UNIX

  • Class 1 Slides
  • Required Reading Prior to Lecture:
    • Part 1 of Unix and Perl Primer for Biologists
  • Topics covered
    • Brief history of computational biology
    • Course computing environment
    • Intro. to UNIX: Part 1
      • Logging in
      • The "shell"
      • "Home"
      • Navigation
      • File system
      • Files
      • Basic commands: ls, pwd, cd, mkdir, head

• Class 2 (Th Jan 11; Layer): Intro to UNIX Part 2

  • Class 2 Slides
  • Required Reading Prior to Lecture:
    • Part 2 (Advanced UNIX) of Unix and Perl Primer for Biologists
  • Topics covered
    • Intro. to UNIX: Part 2
      • grep
      • cut
      • redirects
  • Homework 1 assigned. (due by start of class, Jan 17)

• Class 3 (Tu Jan 16; Quinlan): The human genome

  • Class 3 Slides
  • Required Reading Prior to Lecture:
    • Initial sequencing and analysis of the human genome
  • Topics covered
    • Karyotype
    • Chromosome structure
    • Centromeres
    • Banding
    • Chromatin
    • How was the genome sequenced?
      • sequencing technology
      • assembly strategy
    • Chromosomes
      • size
      • gene content
      • centromeres
    • Haplotypes
    • Genes and transcripts
    • Repeat content
      • mobile elements
      • simple repeats
    • GC content, banding
    • CpG islands

• Class 4 (Th Jan 18; Quinlan): Using UNIX to find patterns in a genome

  • Required Reading Prior to Lecture:
    • None.
  • Topics covered
    • The UNIX PATH
    • Environment variables
    • Basic regular expressions with grep
    • sort
    • uniq
  • Homework 2 (finding biological patterns in FASTA files with UNIX) assigned

• Class 5 (Tu Jan 23; Quinlan): Genetic variation: mutations, polymorphisms, and haplotypes

  • Required Reading Prior to Lecture:
    • A global reference for human genetic variation
  • Topics covered
    • Genetic variation: what, why, etc.
    • Mutation vs. polymorhism
    • De novo mutation
      • Human mutation rates
    • Polymorphism
    • SNPs INDELs
      • abundance
      • frequency
      • examples
      • 1000 Genomes
      • Site frequency spectrum
    • Population stratification
    • Intro to haplotypes and recombination

• Class 6 (Th Jan 25; Quinlan): Modern DNA sequencing technologies

  • Required Reading Prior to Lecture:
    • Coming of age: ten years of next-generation sequencing technologies
  • Topics covered
    • Illumina sequencing
      • Overview of technology
      • Paired-end vs. single-end
    • Pacbio
    • Oxford nanopore
    • Base calling
    • FASTQ format
    • seqtk, fastx toolkit
  • Homework 3 (working with the FASTQ format) assigned

• Class 7 (Tu Jan 30; Quinlan): DNA sequence mapping and alignment](https://docs.google.com/presentation/d/1RskyGhXx4Lc6wSvvb_ZuCUJGUiP2RAr9X8bGh9Kz77I/edit?usp=sharing)

  • Required Reading Prior to Lecture:
    • Alignment of Next-Generation Sequencing Reads
  • Topics covered
    • Sequence alignment
      • Theory
      • Mapping versus alignment
      • Local versus global alignment
        • Smith waterman
        • Needleman-wunsch
      • Advanced algorithms
      • Alignment for RNA-seq
      • Alignment for SV detection.
      • Tools
        • BWA, etc.

• Class 8 (Th Feb 1; Quinlan): SAM/BAM format, samtools, and IGV](https://docs.google.com/presentation/d/1_iT3btOZqjPmVb8Ryk5ssMBCMxoQ0MVmasZ6G0luA-c/edit?usp=sharing)

  • The SAM/BAM format
  • Samtools
  • IGV
  • Homework 4 (creating and working with SAM/BAM files with samtools and IGV) assigned

• Class 9 (Tu Feb 6; Quinlan): SNP and INDEL discovery (part 1)](https://docs.google.com/presentation/d/1D4XY9XxQiyYcwwhomRRONxCPr_bJvcC0WM4sb8vouZM/edit?usp=sharing)

  • Required Reading Prior to Lecture:
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
  • Optional Reading Prior to Lecture:
    • A general approach to single-nucleotide polymorphism discovery.
  • TODO FOR NEXT TIME: INTRODUCE POISSON MODEL OF COVERAGE. 30X IS A DISTRIBUTION
    • https://twitter.com/OmicsOmicsBlog/status/837829111879983104
  • Topics covered
    • SNP and INDEL calling
      • Theory
        • Basic concept
        • Sequencing error
        • Bayes theorem and priors
    • Assigning a genotype
    • Common problems and artifacts
      • paralogy
      • low depth
      • high error rate
      • ambiguous alignment
    • Single sample variant detection

• Class 10 (Th Feb 8; Quinlan): SNP and INDEL discovery (part 2)](https://docs.google.com/presentation/d/12jeJQPbntPPPGYszIH1l9u83mXFVU1XdJw-bNgbFu28/edit?usp=sharing)

  • Required Reading Prior to Lecture:
    • The VCF format and VCFtools
  • Topics covered
    • VCF format
      • Attributes
      • Genotypes
    • Population calling
    • Basic annotations
  • Landscape of human genetic variation
    • Alleles and genotypes
    • Allele frequency spectrum
    • Hardy weinberg equilibrium
    • More on haplotypes and recombination
  • Exploring the format
    • examples
    • IGV
  • Manipulating VCF with bcftools
  • Homework 5 (variant calling and working with VCF files with bcftools and UNIX) assigned

• Class 11 (Tu Feb 13; Quinlan): VCF format, Hardy Weinberg Equilibrium, VCF toolkits

  • Topics covered
    • VCF Format
    • Allele frequencies
    • Genotype frequencies
    • Hardy Weinberg Equilibrium

• Class 12 (Th Feb 15; Quinlan): VCF annotation and interpetation

  • Required Reading Prior to Lecture:
    • Choice of transcripts and software has a large effect on variant annotation
  • Topics covered
    • Concepts
      • e.g, synonymous, non-synonymous
      • frameshift
      • stopgain
      • constraint
      • impact of transcript model
  • Tools
    • Polyphen
    • SIFT
    • vcfanno
    • CADD
    • VEP
    • SnpEff

• Class 13 (Tu Feb 20; Quinlan): Variation in genome structure

  • Required Reading Prior to Lecture:
    • Genome structural variation discovery and genotyping
  • Topics covered
    • The genome is repetitive
    • Segmental duplication
    • SV versus CNV
    • SV Mechanisms
      • NAHR / ectopic recombination
      • NHEJ
      • Replication mechansism
    • SV detection
    • Examples

• Class 14 (Th Feb 22; Quinlan): Somatic mutation in cancer

  • Required Reading Prior to Lecture:
    • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
  • Topics covered
    • Sources of mutation
    • Mutational landscape
    • Tumor heterogeneity
    • Somatic mutation detetion
      • why is it so hard?
    • Using mutation to track cancer evolution
    • Mosaicism and disease

• Class 15 (Tu Feb 27; Quinlan): Genome annotation

  • Required Reading Prior to Lecture:
    • None
  • Topics covered
    • How and why do we annotate a genome?
    • Conservation
    • CpG islands
    • Repeatmasker
    • Chromatin modifications
    • DNA methylations
    • Linkage blocks

• Class 16 (Th Mar 1; Quinlan): Genome data formats and genome arithmetic

  • Required Reading Prior to Lecture:
    • None
  • Topics covered
    • The genome as a coordinate system
    • BED format
    • GFF format
    • VCF format
    • UCSC and Biomart to retrieve genome annotations
    • UCSC and IGV to visualize
    • a bit of awk

• Class 17 (Tu Mar 8; Quinlan): Applied genome arithmetic with bedtools; part 1

  • Required Reading Prior to Lecture:
    • BEDTools: the Swiss‐army tool for genome feature analysis
  • Topics covered
    • The genome as a coordinate system revisited
    • Basic concepts of genome arithmetic
    • Introduction to bedtools
  • Homework 9 (basic genome arithmetic with bedtools) assigned (due Mar 7)

• Class 18 (Th Mar 8; Quinlan): Applied genome arithmetic with bedtools; part 2

• Class 19 (Tu Mar 13; Quinlan): Digging deeper into UNIX, part 1

  • awk
  • sed
  • tr
  • PATH
  • .bashrc

• Class 20 (Th Mar 15; Quinlan): ChIP-seq analysis

  • experimental design
  • protocols
  • examples

• Spring Break March 18-25

• Class 21 (Tu Mar 27; Quinlan): RNA-seq analysis

  • analyses
  • toolsets
  • Class project assignment

• Class 22 (Th Mar 29; Quinlan): Basic probability

  • Probability with coins and dice
  • Probability with DNA
  • Conditional probabilities
  • Use R for examples

• Class 23 (Tu Apr 3; Quinlan): Statistical tests

  • Gaussian
    • Z scores
  • Chi-squared
  • Fisher
  • KS test
  • Rank tests
  • Applications

• Class 24 (Th Apr 5; Quinlan): How do I know if my observation is significant?

  • Models
  • Expectation
  • Tests for significance

• Class 25 (Tu Apr 10; Quinlan): Data visualization, part 1

  • Why
  • Pattern recognition
  • Detect problems
  • Ansombe’s quartet
  • Introduce class projects

• Class 26 (Tu Apr 12; Quinlan): Data visualization, part 2

  • http://www.nature.com/collections/qghhqm/pointsofsignificance
  • Scatter plots
  • Histograms
  • Box whiskers

• Class 27 (Tu Apr 17; Quinlan): Advanced topics

  • loops
  • shuffling
  • randomization
  • advanced commands
  • basic scripts and pipelines

• Class 28 (Th Apr 19; Quinlan): Group Presentations, part 1

• Class 29 (Tu Apr 24; Quinlan): Group Presentations, part 2