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https://github.com/quinlan-lab/applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020
https://github.com/quinlan-lab/applied-computational-genomics
Last synced: 6 days ago
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Applied Computational Genomics Course at UU: Spring 2020
Host: GitHub
URL: https://github.com/quinlan-lab/applied-computational-genomics
Owner: quinlan-lab
License: cc-by-sa-4.0
Created: 2016-08-09T02:10:20.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2024-04-05T20:52:29.000Z (8 months ago)
Last Synced: 2024-08-03T23:12:20.711Z (4 months ago)
Language: HTML
Homepage:
Size: 28.2 MB
Stars: 932
Watchers: 88
Forks: 204
Open Issues: 8
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project

awesome-bioinformatics-education - Applied Computational Genomics Course at UU: Sprint 2022
README

        ### Applied Computational Genomics Course at UU: Spring 2024

- 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 `#general` in the course Slack :

    - Reilly Falter: Weds, 3-4 PM

    - Scott Pew: Mons, 10-11 AM

### 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.**

### Important notes

1. Class participation is expected. Ask a question if you have one!

### 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

- Jan 9, 2024: Introductions, course overview,  connecting to server

    - [slides](https://docs.google.com/presentation/d/1B8kvetTDwUe-d7hZuV2NufVOMPM7MCxh_MyP-n9yDZo/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=idl6oq-MxbM)

- Jan 11, 2024: Intro to Unix

    - [slides]([https://docs.google.com/presentation/d/1YSXYqCSHUZGRVr00oTttv_v1u83ccPLpF5_TMtW0iRI/edit?usp=sharing](https://docs.google.com/presentation/d/1B8kvetTDwUe-d7hZuV2NufVOMPM7MCxh_MyP-n9yDZo/edit?usp=sharing))

    - [youtube](https://www.youtube.com/watch?v=GIGIUMBumME)

- Jan 16, 2024: Intro to Unix, Part 2

    - [slides](https://docs.google.com/presentation/d/1YSXYqCSHUZGRVr00oTttv_v1u83ccPLpF5_TMtW0iRI/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=GIGIUMBumME)

    - 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.txt` to this [link](https://uofu.app.box.com/f/40d8f73cdcdc4c23b6fc3788e1983c6d)

- Jan 18, 2024: More Unix, The Human Genome

    - [slides](https://docs.google.com/presentation/d/1304Ueup_n8_vqKjQZh-AV3dDAOs2gCqNgrm8o25nBHo/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=yPlpVIsaRCg)

- Jan 23, 2024: Finding patterns in the human genome

    - [slides](https://docs.google.com/presentation/d/1W7bwMLAqCIB9unbv4Kswc8P7cE5ATkMhHYJfwBa64L0/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=ngpwuFh7H5M)

- Jan 25, 2024: DNA sequencing technologies

    - [slides](https://docs.google.com/presentation/d/1N0DO5rlHdbrnNhyDhib8fpYYhfbtFOPcKw_Bpvv-2lA/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=fgbk732NdWI)

- Jan 30, 2024: Then FASTQ Format

    - [slides](https://docs.google.com/presentation/d/1N0DO5rlHdbrnNhyDhib8fpYYhfbtFOPcKw_Bpvv-2lA/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=fgbk732NdWI)

- Feb 1, 2024: Sequence mapping and alignment

    - [slides](https://docs.google.com/presentation/d/1RskyGhXx4Lc6wSvvb_ZuCUJGUiP2RAr9X8bGh9Kz77I/edit?usp=sharing)

    - [youtube](https://youtu.be/QuuKYEp5EUA)

    - 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.txt` to this [link](https://uofu.app.box.com/f/ea64f0521a0643fcb77661d1772de01e)

- Feb 6, 2024: SAM/BAM format, samtools, IGV

    - [slides](https://docs.google.com/presentation/d/1_iT3btOZqjPmVb8Ryk5ssMBCMxoQ0MVmasZ6G0luA-c/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=XU8atPxM0VQ)

- Feb 8, 2024: SAM/BAM format, samtools, IGV, continued

    - [slides](https://docs.google.com/presentation/d/1_iT3btOZqjPmVb8Ryk5ssMBCMxoQ0MVmasZ6G0luA-c/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=XU8atPxM0VQ)

- Feb 13, 2024: Genetic Variation

    - [slides](https://docs.google.com/presentation/d/1JnBiaGG_eJAb1LGUiNaXP4DX-oZKaxaDVg1KFqYeAfA/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=N8nTiBOSsHI)

- Feb 15, 2024: SNP and INDEL discovery, binomial random variables

    - [slides](https://docs.google.com/presentation/d/1D4XY9XxQiyYcwwhomRRONxCPr_bJvcC0WM4sb8vouZM/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=2ro9WCOpQqI)

- Feb 20, 2024: Poisson Processes in Biology

    - [slides](https://docs.google.com/presentation/d/18TdXaBIuxi0fmbTKREUH5ogwxIabKlFU9UPhhazEOf8/edit?usp=sharing)

    - [youtube](https://youtu.be/zS13juQqsFU)

    - 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.txt` to this [link](https://uofu.app.box.com/f/570e317e71ba4ff1afdbe296a93f3dbd)

- Feb 22, 2024: VCF format and tools

    - [slides](https://docs.google.com/presentation/d/1kt2br-ZcDIzRqx__oTdC8i4NlAhluWX2WsPT_clqMaI/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=FZtWnNghRkA)

- Feb 26, 2024: VCF annotation and interpetation

    - [slides](https://docs.google.com/presentation/d/1DN99IgciDD05b5Ve_Eaym0ORPhuDFAPU1fXBPoOq5Vo/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=M8UfW8RNTKI)

- 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.txt` to this [link](https://uofu.app.box.com/f/c2b1c395bed14d198ca83e8f1dae39e5)

- Apr 4, 2024: Introduction to generalized linear models (GLMs)

    - [slides](slides/applied_comp_gen.html)

      - **Note:** interactive HTML version of slides can be downloaded from GitHub (click the "Download raw file" button at the page linked above, or `wget` [this link](https://github.com/quinlan-lab/applied-computational-genomics/raw/master/slides/applied_comp_gen.html)) and opened on your personal computer 

### Out of Date, Ignore for now

- [reading assignment: 01-Brief-History-of-Bioinformatics.pdf](articles/01-Brief-History-of-Bioinformatics.pdf)

- [reading assignment: 02-Human-Genome-Review.pdf](articles/02-Human-Genome-Review.pdf)

- Jan 18, 2022: Intro to UNIX, Part 3 and Intro to the Human Genome

    - [slides](https://docs.google.com/presentation/d/1304Ueup_n8_vqKjQZh-AV3dDAOs2gCqNgrm8o25nBHo/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=yPlpVIsaRCg)

    - Homework #1: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw1-md

        - due Jan 25 at 11:59PM

        - post answers as `UNID.hw1.txt` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59)

- Jan 20, 2022: Pattern searching in the human genome

    - [slides](https://docs.google.com/presentation/d/1W7bwMLAqCIB9unbv4Kswc8P7cE5ATkMhHYJfwBa64L0/edit?usp=sharing)

    - [youtube](https://youtu.be/ngpwuFh7H5M?t=22)

- Jan 25, 2022: Pattern searching in the human genome and Intro to Data Analysis in RStudio

    - [slides](https://docs.google.com/presentation/d/1KAwoHV03d4eZ6StXmT-ihvZDCzuiXVUaH6C9SOySjhA/edit?usp=sharing) 

    - [youtube](https://www.youtube.com/watch?v=Gs4XIPknksc)

- Jan 27, 2022: Data frames and Importing Data 

    - [slides](https://docs.google.com/presentation/d/12Fq7OaLR7sdfQ4DvS5qEUcQiWteEtc87JNgHJPRtv88/edit?usp=sharing)

    - Homework #2: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw2-md

        - due Feb 3 at 11:59PM

        - post answers as `UNID.hw2.txt` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59)

- Feb 1, 2022: More with data frames, precision v. accuracy, very basic RNA-seq analysis

    - [slides](https://docs.google.com/presentation/d/1-AMIHxuEuU1JJ_RkActGi5F8bv_R9EWBWWas2eh6AuY/edit?usp=sharing)

    - [video](https://youtu.be/yc3HH8Dxhf8)

- Feb 3, 2022: Intro to the tidyverse (guest lecturer: Charlie Murtaugh)

    - [slides](https://docs.google.com/presentation/d/1KpudXaBqi4FtsVTVJDqD8ChqX3M44REs/edit?usp=sharing&ouid=107526144078068918726&rtpof=true&sd=true)

- Feb 8, 2022: DNA sequencing technologies

    - [slides](https://docs.google.com/presentation/d/1N0DO5rlHdbrnNhyDhib8fpYYhfbtFOPcKw_Bpvv-2lA/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=fgbk732NdWI)

    - Homework #3: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw3-md

        - due Feb 17 at 11:59PM

        - post answers as `UNID.hw3.html` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59)

- Feb 10, 2022: FASTQ format and tools

    - [slides](https://docs.google.com/presentation/d/1N0DO5rlHdbrnNhyDhib8fpYYhfbtFOPcKw_Bpvv-2lA/edit?usp=sharing)   

- Feb 15, 2022: Sequence mapping and alignment

    - [slides](https://docs.google.com/presentation/d/1RskyGhXx4Lc6wSvvb_ZuCUJGUiP2RAr9X8bGh9Kz77I/edit?usp=sharing)

    - [youtube](https://youtu.be/QuuKYEp5EUA)

- Feb 17, 2022: Sequence alignment and SAM/BAM format samtools, and IGV

    - [slides](https://docs.google.com/presentation/d/1_iT3btOZqjPmVb8Ryk5ssMBCMxoQ0MVmasZ6G0luA-c/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=XU8atPxM0VQ)

- Feb 22, 2022: Samtools and IGV

    - [slides](https://docs.google.com/presentation/d/1_iT3btOZqjPmVb8Ryk5ssMBCMxoQ0MVmasZ6G0luA-c/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=XU8atPxM0VQ)

- Feb 24, 2022: Poisson Processes in Biology

    - [slides](https://docs.google.com/presentation/d/18TdXaBIuxi0fmbTKREUH5ogwxIabKlFU9UPhhazEOf8/edit?usp=sharing)

    - [youtube](https://youtu.be/zS13juQqsFU)

- March 1, 2022: Uncertainty in RNA-seq data 

    - [slides](https://docs.google.com/presentation/d/1KMVLhMSqTPcsRkflvNFif6xCp_lnkAF_V73S61b0DyY/edit?usp=sharing)

    - [youtube](https://youtu.be/xItNEtQvYaU)

- March 3, 2022: An introduction to awk and bioawk

    - [slides](https://docs.google.com/presentation/d/1ZfLRLxpc12YqeCt8DWojNwKUuW1WZSp_uTXPK2g2e3o/edit#slide=id.p)

    - [youtube](https://youtu.be/iiFhBvA_wfA) 

- Homework #4: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw4-v3-md

    - due Mar 24 at 11:59PM

    - post answers as `UNID.hw4.txt` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59)

- Mar 15, 2022: Genetic Variation

    - [slides](https://docs.google.com/presentation/d/1JnBiaGG_eJAb1LGUiNaXP4DX-oZKaxaDVg1KFqYeAfA/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=N8nTiBOSsHI)

- Mar 17, 2022: SNP and INDEL discovery (part 1)

    - [slides](https://docs.google.com/presentation/d/1D4XY9XxQiyYcwwhomRRONxCPr_bJvcC0WM4sb8vouZM/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=2ro9WCOpQqI)

- Mar 22, 2022: Rates and patterns of human germline variation

    - [slides]()

    - [youtube]()

- Mar 24, 2022: VCF format, Hardy Weinberg Equilibrium, VCF toolkits

    - [slides](https://docs.google.com/presentation/d/1kt2br-ZcDIzRqx__oTdC8i4NlAhluWX2WsPT_clqMaI/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=FZtWnNghRkA)

- Mar 29, 2022: VCF annotation and interpetation

    - [slides](https://docs.google.com/presentation/d/1DN99IgciDD05b5Ve_Eaym0ORPhuDFAPU1fXBPoOq5Vo/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=M8UfW8RNTKI)

- Homework #5: https://gist.github.com/arq5x/c0eb84bce2086fbfbe9184668ef87b31#file-hw5-2022-md

    - due Mar 18 at 11:59PM

    - post answers as `UNID.hw5.txt` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59) -->

- Mar 31, 2022: Genome Annotation and Resources

    - [slides](https://docs.google.com/presentation/d/1PU4ADdlmZu9jOkUa_FgrS5ppTJ3CsCIXwn1W9WkzApI/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=ElnZGlzb4qo)

- April 5, 2022: Genome Annotation Formats.

    - [slides - 1](https://docs.google.com/presentation/d/1Eylp9pcU8xEhyBJJvL57pSjSukQdhBnG1sWCvJlCngs/edit?usp=sharing)

    - [slides - 2](https://docs.google.com/presentation/d/1yXFB72CHPiVH8zCKBwBOQg-ssmzS9xUOcTNhcsQgV1c/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=tq3GeDXbZXA)

- April 7, 2022: Genome arithmetic with bedtools

    - [bedtools tutorial](http://quinlanlab.org/tutorials/bedtools/bedtools.html)

    - [bedtools docs](https://bedtools.readthedocs.io/en/latest/index.html#)

    - [youtube](https://www.youtube.com/watch?v=1R1KocKEzYY)

- Apr 12, 2022: Real world analyses with bedtools.

    - [slides](https://docs.google.com/presentation/d/1-LR5tHGbvJtmk5rdyBihzd_9viI15KnTtFOrmAHdjsc/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=qV6Iv1Dco-M)

- 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.txt` to this [link](https://uofu.app.box.com/f/462f5bfaaeb14f8ebb2b3c25f0cfab59)

- Apr 14, 2022: Monte Carlo simulations and more on UNIX

    - [slides 1](https://docs.google.com/presentation/d/1-LR5tHGbvJtmk5rdyBihzd_9viI15KnTtFOrmAHdjsc/edit?usp=sharing)

    - [slides 2](https://docs.google.com/presentation/d/186g0U-3M-Cy-wznAoFT6WwpgQCvYwmnegrr8UJ7vIJo/edit#slide=id.p)

    - [youtube - Monte Carlo](https://youtu.be/QQ94LZ-gWqM)

    - [youtube - bash_profile](https://youtu.be/zearEb3guLI)

- Apr 19, 2022: The Normal Distribution

    - [slides](https://docs.google.com/presentation/d/1e1cF_fPRtrZvr1Y8N_Kat4o_Ds0QOStIvJDXC2mcy0Q/edit#slide=id.g82b15b332d_0_0)

- Apr 21, 2022: Descriptive plots. The Central Limit Theorem

    - [slides 1](https://docs.google.com/presentation/d/1bcZKEh-nEq-ELVBMY9NYy4a0Ue5glAk0y17CywY9K1w/edit#slide=id.p)

    - [slides 2](https://docs.google.com/presentation/d/1Weh4t69BeEe8rCFXEsfwlOdhX-wV7I8ceePvwXbUCsc/edit?usp=sharing)

- April 26, 2022:  The t-statistic, t-distribution, t-tests, and p-values

    - [slides](https://docs.google.com/presentation/d/1X1l4UYxEzarF69W5p8PofQiAEoFNOqDlFBBppIfUc_w/edit)

    - [youtube](https://www.youtube.com/watch?v=golFyEZhVa8&feature=youtu.be)

Not covered in 2022's course, but available for reference.

- Apr 13, 2020: Q-Q plots

    - [slides](https://docs.google.com/presentation/d/1e1cF_fPRtrZvr1Y8N_Kat4o_Ds0QOStIvJDXC2mcy0Q/edit#slide=id.g82b15b332d_0_0)

- April 22, 2020:  Introduction to Linear Regression

    - [slides](https://docs.google.com/presentation/d/1ugkYc24AmKVEO0-x-M3qZ4EsSIedbSwyqD6cLN0YIiI/edit#slide=id.gd42443b26c_0_0)

    - [youtube](https://www.youtube.com/watch?v=KekLyPeet3k)

- April 27, 2020:  Introduction to tidyverse

    - [slides](https://docs.google.com/presentation/d/1tdQ5B7LhiAE5-G6sJ6nDeCna463dWjKlAenc5DCde0g/edit#slide=id.p1)

    - [youtube]

- The Central Limit Theorem and Confidence Intervals

    - [slides](https://docs.google.com/presentation/d/1Weh4t69BeEe8rCFXEsfwlOdhX-wV7I8ceePvwXbUCsc/edit?usp=sharing)

- Structural and copy number variation

    - [slides](https://docs.google.com/presentation/d/1h_MApL1p21ye0doXDIJdx8snix1VQInyPZKjPT0AhFM/edit?usp=sharing)

    - [youtube](https://www.youtube.com/watch?v=Skfzw5LwJq0)

- Patterns of Mutation in the Human Genome

    - [slides](https://drive.google.com/file/d/1qWJysIa1XAFZ_qH-kOVRDbXKGt9e9lFZ/view?usp=sharing)