HTS2019

Slides

  • Slide sets

Quick Intro of Analysis Tools

  • Duke HTS Summer Course 2019
  • Introduction to Unix and bash
  • Introduction to R
  • R libraries and Bioconductor
  • Hands-On Tidyverse - with count data
  • Simulations and Statistical Inference
  • Estimation and Hypothesis Testing

Unix Shell

  • Working with Unix
  • File I/O
  • File archival and recovery
  • Working with text
  • Unix Variables
  • Using bash in bioinformatics
  • Unix capstone exercise
  • Unix capstone exercise
  • The Unix Shell: Regular Expressions
  • Unix Review of Basics

R Graphics and Data Manipulation

  • Basics of R (Review)
  • Basics of R (Review)
  • Data Manipulation in the tidyverse
  • Tidy Data
  • File I/O
  • Unsupervised Learning
  • Unsupervised Learning
  • R Graphics
  • R Graphics
  • R Graphics
  • R Graphics Exercise
  • R Graphics Exercise (Solutions)

Bioinformatics (FASTQ, FASTQC, STAR, etc)

  • Introduction to FASTQ Files
  • What do quality scores mean?
  • What do quality scores mean?
  • Quality Control
  • Trimming and Filtering a FASTQ
  • Trimming and Filtering
  • Download and Index Genome
  • Counting Reads
  • Mapping Reads to a Reference Genome
  • Making Generic Commands
  • Making a Pipeline
  • Working with Loops
  • Working with Loops
  • Looping with Globs
  • Initialize Variables and Make Directories
  • Make adapter file
  • Download and Index Genome
  • Prepare Data
  • Downloading Everything
  • Using IGV
  • Run with shorter intron limit

Analysis of Pilot Data (Gene Count, DESeq2 & DE Analysis)

  • Get Star Count of the Pilot 2019 Data
  • DESeq2: Create count matrix and metadata data frame
  • DESeq2: Create Data Objects
  • DESeq2: Basic Differential Expression (DE) analysis
  • DESeq2: Basic Differential Expression (DE) analysis
  • Generate figures from DESEq2 analysis

Reproducible Analysis (Git)

  • Data handling Demo
  • Git Lesson
  • Git in class

After the course... (Docker & Singularity)

  • Overview
  • High Priority
  • Maintaining Personal Files
  • Accessing Course Material
  • Docker Containers
  • Select Duke Computing Resources
  • Assorted Notes on Approaches to Reproducible Analysis
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