GEN220_2019

GEN220: Highthroughput Biological Data Analysis - Fall 2019

See the Syllabus PDF for an overview of lecture topics.

Examples worked during class will be uploaded in this working repository. To check it out and keep it update.

git clone https://github.com/biodataprog/GEN220_2019_examples.git
cd GEN220_2019_examples
# ... time passes, new examples are uploaded
git pull # to get the latest version of the files

Resources

• SSH keys
• Github workflows and Software Carpentry Github Tutorial
• Software Carpentry UNIX/Shell Novice Tutorial
• UNIX command reference 1
• UNIX command reference 2
• Shell Scripting Tutorial
• Intro to Command-Line from HPCC Major Topic Areas
• UNIX Shell scripting and using HPCC
• Python Programming
• Bioinformatics analysis methods
• Editors VIM/VI Nano Emacs Emacs Manual

Homework

• HW1 - Homework 1 PDF
• HW2 - Homework 2 PDF - Due Nov 1 (12:00 Noon)
• HW3 - Homework 3 PDF - Due Dec 4

Project

• Project Team Ideas Project

Lectures

• 0 & 1 Course Intro / UNIX I: Cmdline PDF
• 2 UNIX 2: Running Tools PDF
• 3 UNIX 3: Analysis and Programming PDF

• 4 UNIX 4: Misc Tricks PDF

• 5 Python 1: Intro PDF
• 6 Python 2: Logic,Loops,IO PDF
• 7 Python 3: Dictionaries and Functions PDF
• 7 Python 4: Workshop PDF
• 8 Python 5: Regular Expressions PDF

• 9 Python 6: Packages/BioPython PDF

• 10 Bioinformatics 1: Basics and BLAST PDF
• 11 Bioinformatics 2: Orthologs PDF
• 12 Bioinformatics 3: Ranges PDF
• 13 Bioinformatics 4: Workshop - parsing PDF
• 14 Bioinformatics 5: RNASeq PDF
• 15 Bioinformatics 6: Protein domains PDF
• 16 Bioinformatics 7: R basics - we will use Rstudio for this http://rstudio.hpcc.ucr.edu on-line or you can use it locally on your laptop if you have installed.
• • Also see https://datacarpentry.org/R-genomics/05-data-visualization.html
• 17 Bioinformatics 8: Short Reads PDF