HTS2018

Slides

  • Slide sets

Unix Shell

  • Duke HTS Summer Course 2018
  • Introduction to Unix and bash
  • Bash Scratchpad
  • The Unix Shell: File and Directory Management
  • The Unix Shell: Working with Text
  • The Unix Shell: Finding Stuff
  • The Unix Shell: Regular Expressions
  • The Unix Shell: Writing Shell Scripts
  • The Unix Shell: Exercises with Solutions
  • Using bash in bioinformatics
  • Bash Exercise (Solutions)
  • Bash Exercise 2: Working with a GTF file (Solutions)

Bioinformatics

  • 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
  • Mapping Reads to a Reference Genome
  • Hands On Bioinformatics Exercise #1
  • Counting Reads
  • Working with Paired-Reads
  • Making Generic Commands
  • Making a Pipeline
  • Working with Loops
  • Working with Loops
  • Looping with Globs
  • Hands On Bioinformatics Exercise #2
  • Prepare Data
  • Downloading Everything
  • Using IGV
  • Run with shorter intron limit
  • Hands On Bioinformatics Exercise #3
  • Demultiplex a Raw FASTQ
  • Raw Data
  • Bash Functions

Analysis of Pilot Data

  • Set up environment
  • Read in results
  • Check the label between metadata and mapping results
  • Construct gene count matrix for each library
  • Metadata
  • Store the results
  • Visualize the mapping results
  • The End

R Graphics and Data Manipulation

  • Introduction to R
  • R Graphics
  • R Graphics
  • R Graphics
  • R Graphics Exercise (Solutions)
  • Using dplyr for data manipulation
  • Using tidyr to create tidy data sets
  • Working with multiple files

R Statistical Analysis

  • Simulations and Statistical Inference
  • Estimation and Hypothesis Testing
  • Unsupervised and Supervised Learning
  • Unsupervised Learning
  • Supervised Learning

Bioconductor

  • R libraries and Bioconductor
HTS2018
  • Docs »
  • Bioinformatics Table of Contents
  • View page source

Bioinformatics Table of Contents¶

Week 2, Day 5 (7/13/2018)¶

  1. Lecture Slides: Lab Followup
  2. Lecture Slides: Bioinformatics Pipeline
  3. Introduction to FASTQs
    • Quality Scores
  4. Quality Control
  5. Trimming and Filtering
  6. Download and Index Genome
  7. Mapping Reads to a Reference Genome
  8. Hands On Exercise #1

Week 4, Day 1 (7/23/2018)¶

  1. Counting Reads
  2. Working with Paired Reads
  3. Making Generic Commands
  4. Making a Pipeline
  5. Pipeline in a Loop
  6. Running Multiple FASTQs
  7. Looping with Globs
  8. Hands On Exercise #2

Week 4, Day 2 (7/24/2018)¶

  • IGV visualization
    • Shorter Introns
  1. Hands On Exercise #3

Appendix¶

  • Demultiplex Raw FASTQs
  • Bash Functions

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