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The purpose of this site is to provide a resource for students and instructors participating in the course. Its easier for me to update and build labs than Canvas.
Additional information about absences due to COVID-19
The ACF has been rebranded to ISAAC. ISAAC has a new website.
Log in
ssh username@duo.acf.tennessee.edu
Get an interactive node with only 2Gb of RAM
qsub -I -A ACF-UTK0138 -q debug -l walltime=1:00:00,nodes=1:ppn=1,advres=epp622.13776185
Get an interactive node with 4Gb of RAM
qsub -I -A ACF-UTK0138 -q debug -l walltime=1:00:00,nodes=1:ppn=2,advres=epp622.13776185
or if the reservation isn't working or is full
qsub -I -A ACF-UTK0138 -q debug -l walltime=1:00:00,nodes=1:ppn=2
For beacon nodes the amount of memory per core is 16G, so use feature=beacon and ppn=1 to get the minimum of 16 GB memory:
qsub -I -A ACF-UTK0138 -q debug -l walltime=1:00:00,nodes=1:ppn=1,feature=beacon
Go to your folder in the course directory:
/lustre/haven/proj/UTK0138/yourusername
Load python
module load python/3.6.1
- Video: Syllabus Overview and how this course will work
- Video: Introduction to the course, what is computational genomics, and why learn Linux?
- Lab:
- Introduce Beant Kapoor, our TA
- Attendance
- Slack is super awesome
- Instructions: Register for the ACF and get a shell on your laptop
- Readings:
- So you want to be a computational biologist? Loman and Watson, 2013
- A brief history of bioinformatics Gauthier et al 2019
- Lecture: Video: Computers and high-performance computing
- Lab: Shell I
- Lecture: Video: Managing data and projects for reproducibility
- Lab: Shell II
- Reviewing relative and absolute paths
- See above for ACF login instructions
- Continuing Lessons from SWC
- A1 assigned - Find on Canvas under "Quizzes". Due in 1 week!
- Readings:
- Ten Simple Rules for Digital Data Storage Hart et al. 2016
- A Quick Guide to Organizing Computational Biology Projects Noble 2009
- list of commands we have learned so far
- Lecture: FAIR Principles and Databases for Genomic Data
- Lab: Shell III
- Finish Up - SWC Pipes and Filters
- SWC - Loops
- Video of lab session
- Survey 1 - https://forms.gle/4ZnegTQXNL6KkccR7
- Reading:
- The FAIR Guiding Principles for scientific data management and stewardship Wilkinson et al 2016
- Lecture: Introduction to Sequence Alignment
- Lab:
- Don't forget the survey
- A2 assigned
- A1 due
- Lecture: High throughput sequencing
- Video of lecture
- Slides
- My dogs have something to say about that video:
- Learn about sequencing chemistries from the companies:
- Survey Results are In! Thanks to all who responded, and here are some of my thoughts on Survey 1
- Lab: Shell IV
- Finish up SWC - Loops
- SWC - Shell Scripts
- Recording of lab
- Paper to learn more:
- van Dijk et al. 2018 The Third Revolution in Sequencing Technology
- Lecture: DNA sequencing, quality control and trimming
- Recording from Meg
- Slides
- Recording from Ryan Kuster - Lots more info on fastq and trimming - I learned a lot from this!
- Lab:
- FastQC Lab
- FastQC software website
- SCP Slides
- FastQ Reference
- FastQ Reference with the missing ones from above - see the Q value on the leftmost column
- A3 assigned
- A2 due
- Papers to learn more:
Scholarship requires thoughtfulness about the society in which our science takes place, and how that society shapes, steers, or, in some cases, impedes the best science and best outcomes for individual scientists. In tandem with a national teach-in about racism, I'd like to provide you with resources on the impact of racism and injustice and also how we can all personally contribute to positive change. These are thought-provoking materials specifically related to being in academia and/or at UTK, and in many cases link to peer-reviewed literature on both the existence of racism and its harmful impacts.
- UT’s STRIDE program has a list of published papers on race and gender found here as well as a slide deck on how UT is trying to recruit and improve diversity and excellence on campus
- PNAS and prejudice, by National Medal of Science winner, and editor-in-chief of PNAS Dr. May Berenbaum
- NIH Director’s Message regarding racism and mental health research
- A customized belonging intervention improves retention of socially disadvantaged students at a broad-access university- Murphy et al. 2020
-
Presumed Incompetent: The Intersections of Race and Class for Women in Academia edited by Gabriella Gutiérrez y Muhs, Yolanda Flores Niemann, Carmen G. González, Angela P. Harris
- A compilation of 40 stories and studies about the intersecting roles of race, gender, and class in the working lives of women faculty of color.
-
Does STEM Stand Out? Examining Racial/Ethnic Gaps in Persistence Across Postsecondary Fields - Riegle-Crumb, King, & Irizarry (2019)
- National study showing that “Black and Latina/o youth who begin college as STEM majors are more likely to depart than their White peers.”
-
Is Science for Us? Black Students’ and Parents’ Views of Science and Science Careers - Archer, Dewitt, & Osborne (2015)
- Draws on survey data to address “why science careers are less ‘thinkable’ for young black students” and considers implications for science education.
-
How Gender and Race Stereotypes Impact the Advancement of Scholars in STEM: Professors’ Biased Evaluations of Physics and Biology Post-Doctoral Candidates - Eaton et al. (2019)
- Study showing that the perceived race and gender of a postdoctoral applicant’s name affects how an otherwise-identical CV is judged.
- Lecture: Read mapping
- Lab: DNA II - Read trimming
- Trimmomatic Lab Instructions
- Lab Recording
- Trimmomatic home page
- Reading/Additional Resources
- Canzar and Salzberg 2017 Short Read Mapping: An Algorithmic Tour
- Ben Langmead (author of bowtie) on YouTube:
- Some historical context from Lior Pachter's blog
- SAM format specs
- Decipher the SAM flag
Learn how to register, vote by mail, see a sample ballot and more.
- Lecture: ACF batch job submission
- ACF Guest Speaker
- Recording of Nic Csercsevits from the ACF (see time 8:28 to 27:22) - then the lab fails because the ACF is down and the rest is a long help session
- Lab: DNA III - Read mapping
- A3 due
- Reading:
- Lecture: Variant Calling
- Lab: DNA IV - Variant Calling
- Reading
- Nielson et al 2011 Genotype and SNP calling from next-generation sequencing data - A bit older but still great for learning the basic concepts
- Hwang et al 2015 Systematic comparison of variant calling pipelines using gold standard personal exome variants - Mentioned in lecture
- Test 1 Assigned
- No Lecture/Lab - Work on Test 1
- Very short Q&A session
- No Lecture/Lab - Work on Test 1
- Q&A about Test 1 with many helpful topics
- Python I
-
Python for Biologists
- Today we'll cover:
- Introduction
- Printing and Manipulating Text
- Recording
- Python II
- Continuing with Python for Biologists
- Finish up last bit of Printing and Manipulating Text
- Working with Files
- Recording
- I put the python book as a pdf in the course files on canvas. Please look at the questions at the end of the chapter, they will be essential to answering the quiz questions. For 'Printing and Manipulating Text' the exercises are on pages 36-38 and the solutions are on pages 39-51.
- Python III
- Continuing with Python for Biologists
- Test 1 Due
- A4 assigned
- Python IV
- Continuing with Python for Biologists
- Survey 2
- Early voting starts today! If you are registered in TN, check out these Vols Vote resources.
- Responses to Survey 2
- Python V
- Continuing with Python for Biologists
- Conditional Tests
- Recording
- A5 assigned
- A4 Due
- Python VI
- Recording
- Overview of Github lecture/demo
- Python VI
- A5 Due
- Test 2 Assigned
- No Lecture/Lab - Work on Test 2
- No Lecture/Lab - Work on Test 2
- Help Session Recording - Short but a few nice tips on the first problem
- Friday help session
- Lecture: RNASeq Intro
- Lab: RNASeq I - Read trimming
- RNASeq Set Up and Read Trimming Lab Instructions
- Lab Recording
- Reading/Additional Resources
- Li WV, Li JJ. Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quantitative Biology. 2018 Sep 1;6(3):195-209.
- Soneson et al. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences Version 2. F1000Res. 2015; 4: 1521.
- Test 2 Due
- Lecture: RNASeq Project Design and GFF files
- Lab: RNASeq II - Read mapping
- RNASeq Read Mapping and Counting Lab Instructions
- Lab Recording
- Run nano 2.9.8 on ISAAC
- A6 assigned
- Python scripts for Quiz 4 and Quiz 5
- RNASeq III - Normalization and Data Exploration
- Lab: RNASeq III - Read counting and data exploration
- Counting with HTseq and PCAs Lab Instructions
- Lab Recording
- Papers:
- Li WV, Li JJ. Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quantitative Biology. 2018 Sep 1;6(3):195-209.
- Maza E, Frasse P, Senin P, Bouzayen M, Zouine M. Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: a matter of relative size of studied transcriptomes. Communicative & integrative biology. 2013 Nov 9;6(6):e25849.
- Other Sites:
- Harvard Chan Bioinformatics Core RNASeq DEG Workshop
- Material on Normalization
- RNASeq Blog: RPKM, FPKM and TPM, clearly explained. Including video from StatQuest.
- Harvard Chan Bioinformatics Core RNASeq DEG Workshop
- RNASeq IV
- Labs
- Rclone Instructions
- DeSeq2 Instructions
- Recording of lab
- A6 due
- Test 3 coming tomorrow - here's the draft to start looking at
- Resources:
- DESeq2 Paper Love et al 2014
- DESeq2 Vignette
- DESeq2 Manual
- No Lecture/Lab - Work on Test 3
- Course review open!
- Test 2 Answers
- Help Session Recording
- No Lecture/Lab - Work on Test 3
- No Lecture/Lab - Work on Test 3
- No Class Day
- Test 3 due
- Final Survey for Course through SAIS