- Faculty: Aaron Quinlan (aquinlan at genetics.utah.edu)
- Teaching assistants:
- Scott Pew
- Reilly Falter
- Meets Tu and Th from 10:30-11:50 January 9, 2024.
- TA Hours (Zoom links pinned to
#generalin the course Slack :- Reilly Falter: Weds, 3-4 PM
- Scott Pew: Mons, 10-11 AM
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.
- Class participation is expected. Ask a question if you have one!
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.
- Jan 9, 2024: Introductions, course overview, connecting to server
- Jan 11, 2024: Intro to Unix
- slides
- youtube
- Jan 16, 2024: Intro to Unix, Part 2
- slides
- youtube
- Homework #1: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw1-md
- due Jan 25 at 11:59PM
- show all commands used
- post answers in a plain text file as (replace with your UNID)
UNID.hw1.txtto this link
- Jan 18, 2024: More Unix, The Human Genome
- Jan 23, 2024: Finding patterns in the human genome
- Jan 25, 2024: DNA sequencing technologies
- Jan 30, 2024: Then FASTQ Format
- Feb 1, 2024: Sequence mapping and alignment
- slides
- youtube
- Homework #2: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw2-md
- due Feb 13 at 11:59PM
- show all commands used
- post answers in a plain text file as (replace with your UNID)
UNID.hw2.txtto this link
- Feb 6, 2024: SAM/BAM format, samtools, IGV
- Feb 8, 2024: SAM/BAM format, samtools, IGV, continued
- Feb 13, 2024: Genetic Variation
- Feb 15, 2024: SNP and INDEL discovery, binomial random variables
- Feb 20, 2024: Poisson Processes in Biology
- slides
- youtube
- Homework #3: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw3-2024-md
- due Feb 29 at 11:59PM
- show all commands used
- post answers in a plain text file as (replace with your UNID)
UNID.hw3.txtto this link
- Feb 22, 2024: VCF format and tools
- Feb 26, 2024: VCF annotation and interpetation
- Feb 28, 2024: Group Project Introduction
- Apr 2, 2024: Homework #4
- due at 11:59 PM
- post answers in a plain text file as (replace with your UNID)
UNID.hw4.txtto this link
- Apr 4, 2024: Introduction to generalized linear models (GLMs)
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Jan 18, 2022: Intro to UNIX, Part 3 and Intro to the Human Genome
- slides
- youtube
- Homework #1: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw1-md
- due Jan 25 at 11:59PM
- post answers as
UNID.hw1.txtto this link
-
Jan 20, 2022: Pattern searching in the human genome
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Jan 25, 2022: Pattern searching in the human genome and Intro to Data Analysis in RStudio
-
Jan 27, 2022: Data frames and Importing Data
- slides
- Homework #2: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw2-md
- due Feb 3 at 11:59PM
- post answers as
UNID.hw2.txtto this link
-
Feb 1, 2022: More with data frames, precision v. accuracy, very basic RNA-seq analysis
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Feb 3, 2022: Intro to the tidyverse (guest lecturer: Charlie Murtaugh)
-
Feb 8, 2022: DNA sequencing technologies
- slides
- youtube
- Homework #3: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw3-md
- due Feb 17 at 11:59PM
- post answers as
UNID.hw3.htmlto this link
-
Feb 10, 2022: FASTQ format and tools
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Feb 15, 2022: Sequence mapping and alignment
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Feb 17, 2022: Sequence alignment and SAM/BAM format samtools, and IGV
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Feb 22, 2022: Samtools and IGV
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Feb 24, 2022: Poisson Processes in Biology
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March 1, 2022: Uncertainty in RNA-seq data
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March 3, 2022: An introduction to awk and bioawk
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Homework #4: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw4-v3-md
- due Mar 24 at 11:59PM
- post answers as
UNID.hw4.txtto this link
-
Mar 15, 2022: Genetic Variation
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Mar 17, 2022: SNP and INDEL discovery (part 1)
-
Mar 22, 2022: Rates and patterns of human germline variation
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Mar 24, 2022: VCF format, Hardy Weinberg Equilibrium, VCF toolkits
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Mar 29, 2022: VCF annotation and interpetation
-
Homework #5: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw5-2022-md
- due Mar 18 at 11:59PM
- post answers as
UNID.hw5.txtto this link -->
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Mar 31, 2022: Genome Annotation and Resources
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April 5, 2022: Genome Annotation Formats.
- April 7, 2022: Genome arithmetic with bedtools
- Apr 12, 2022: Real world analyses with bedtools.
- Homework #6: solve all 10 puzzles at the end of the bedtools tutorial: http://quinlanlab.org/tutorials/bedtools/bedtools.html
- due April 26 (last day of classes at 11:59PM
- post answers as
UNID.hw6.txtto this link
- Apr 14, 2022: Monte Carlo simulations and more on UNIX
- Apr 19, 2022: The Normal Distribution
- Apr 21, 2022: Descriptive plots. The Central Limit Theorem
- April 26, 2022: The t-statistic, t-distribution, t-tests, and p-values
Not covered in 2022's course, but available for reference.
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Apr 13, 2020: Q-Q plots
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April 22, 2020: Introduction to Linear Regression
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April 27, 2020: Introduction to tidyverse
- slides
- [youtube]
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The Central Limit Theorem and Confidence Intervals
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Structural and copy number variation
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Patterns of Mutation in the Human Genome