Ideas to implement or to icebox but get out of your head.
Introduction
- Introduction
- Preface
- what is bioinformatics
- Data Terminology
- Sequencing Technologies
- File Formats
Experimental Design
This section could be skipped if they want to start working right away
- Introduction to Experimental Design
- Learning Objective
- What is your biological question?
- Biological system
- Sequencing technology
- Funding and cost
- prelude to examples
- Examples
- Sex determination
- Seriola 90 fish experiment.
- Genome Assembly
- Seriola dorsalis genome
- Red abalone genome
- Teosinte genome
- Wasp genome
- metagenome
- Genome Annotation
- 16S
Data Acquisition
- What dataset will we use throughout this text
- Why Arabidopsis
- How to download our primary dataset
- Where to find and download data? fastq, fasta, genome, etc
- sra
- geo
- ncbi
- iplant
- etc
- How to transfer Data
- scp
- Rsync
- wget
- globus
Data wrangling
- Review of fasta/fastq file format
- Problems and solutions
- fastq -> fasta
- fastq quality trimming
Data Analysis
- Introduction to Data analysis
-
RNA-Seq Analysis
- RNA-Seq Analysis (intro)
- Arabidopsis with a genome
- Which genes are significant?
- Arabidopsis without a genome
- Which genes are significant?
- Comparison of Arabidopsis with and without a genome.
- How are the results different?
- Venn diagram of significant genes.
- How are they the same?
- Example 2
- Example 3
- Genome Assembly
- introduction to Genome assembly
- List of assembly programs
- How to pick a genome assembly programs
- Assumptions and limitations of domain and data.
visualization
- Introduction to R
- Introduction to iPython
- Introduction to Cytoscape
Appendix
- Introduction to Unix and Terminals
- Choose your own adventure series. Create a storyline that requires the users to solve problems (real world) using sequencing data. Hospital outbreak, Ebola virus spread, etc.
- Would need them to somehow make choices that would lead them down different paths.
Collection of links to explore
- http://www.tengfei.name/ggbio/docs/man/layout_circle-method.html