Applied Computational Genomics Course at UU: Spring 2020
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#general in the course Slack :
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.
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.
UNID.hw1.txt to this linkUNID.hw2.txt to this linkUNID.hw3.txt to this linkUNID.hw4.txt to this linkJan 18, 2022: Intro to UNIX, Part 3 and Intro to the Human Genome
UNID.hw1.txt to this linkJan 20, 2022: Pattern searching in the human genome
Jan 25, 2022: Pattern searching in the human genome and Intro to Data Analysis in RStudio
Jan 27, 2022: Data frames and Importing Data
UNID.hw2.txt to this linkFeb 1, 2022: More with data frames, precision v. accuracy, very basic RNA-seq analysis
Feb 3, 2022: Intro to the tidyverse (guest lecturer: Charlie Murtaugh)
Feb 8, 2022: DNA sequencing technologies
UNID.hw3.html to this linkFeb 10, 2022: FASTQ format and tools
Feb 15, 2022: Sequence mapping and alignment
Feb 17, 2022: Sequence alignment and SAM/BAM format samtools, and IGV
Feb 22, 2022: Samtools and IGV
Feb 24, 2022: Poisson Processes in Biology
March 1, 2022: Uncertainty in RNA-seq data
March 3, 2022: An introduction to awk and bioawk
Homework #4: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw4-v3-md
UNID.hw4.txt to this linkMar 15, 2022: Genetic Variation
Mar 17, 2022: SNP and INDEL discovery (part 1)
Mar 22, 2022: Rates and patterns of human germline variation
Mar 24, 2022: VCF format, Hardy Weinberg Equilibrium, VCF toolkits
Mar 29, 2022: VCF annotation and interpetation
Homework #5: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw5-2022-md
UNID.hw5.txt to this link -->Mar 31, 2022: Genome Annotation and Resources
April 5, 2022: Genome Annotation Formats.
UNID.hw6.txt to this linkNot covered in 2022's course, but available for reference.
Apr 13, 2020: Q-Q plots
April 22, 2020: Introduction to Linear Regression
April 27, 2020: Introduction to tidyverse
The Central Limit Theorem and Confidence Intervals
Structural and copy number variation
Patterns of Mutation in the Human Genome
197 followers · starred Jan 2017
8 followers · starred Apr 2017
146 followers · starred Jul 2022
22 followers · starred Oct 2017
Applied Computational Genomics Course at UU: Spring 2020
HTML
1,132
223 commits
updated Apr 5, 2024
#general in the course Slack :
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.
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.
UNID.hw1.txt to this linkUNID.hw2.txt to this linkUNID.hw3.txt to this linkUNID.hw4.txt to this linkJan 18, 2022: Intro to UNIX, Part 3 and Intro to the Human Genome
UNID.hw1.txt to this linkJan 20, 2022: Pattern searching in the human genome
Jan 25, 2022: Pattern searching in the human genome and Intro to Data Analysis in RStudio
Jan 27, 2022: Data frames and Importing Data
UNID.hw2.txt to this linkFeb 1, 2022: More with data frames, precision v. accuracy, very basic RNA-seq analysis
Feb 3, 2022: Intro to the tidyverse (guest lecturer: Charlie Murtaugh)
Feb 8, 2022: DNA sequencing technologies
UNID.hw3.html to this linkFeb 10, 2022: FASTQ format and tools
Feb 15, 2022: Sequence mapping and alignment
Feb 17, 2022: Sequence alignment and SAM/BAM format samtools, and IGV
Feb 22, 2022: Samtools and IGV
Feb 24, 2022: Poisson Processes in Biology
March 1, 2022: Uncertainty in RNA-seq data
March 3, 2022: An introduction to awk and bioawk
Homework #4: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw4-v3-md
UNID.hw4.txt to this linkMar 15, 2022: Genetic Variation
Mar 17, 2022: SNP and INDEL discovery (part 1)
Mar 22, 2022: Rates and patterns of human germline variation
Mar 24, 2022: VCF format, Hardy Weinberg Equilibrium, VCF toolkits
Mar 29, 2022: VCF annotation and interpetation
Homework #5: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw5-2022-md
UNID.hw5.txt to this link -->Mar 31, 2022: Genome Annotation and Resources
April 5, 2022: Genome Annotation Formats.
UNID.hw6.txt to this linkNot covered in 2022's course, but available for reference.
Apr 13, 2020: Q-Q plots
April 22, 2020: Introduction to Linear Regression
April 27, 2020: Introduction to tidyverse
The Central Limit Theorem and Confidence Intervals
Structural and copy number variation
Patterns of Mutation in the Human Genome
197 followers · starred Jan 2017
8 followers · starred Apr 2017
146 followers · starred Jul 2022
22 followers · starred Oct 2017