NGS Workshop Tutorials (2011 version)

• Presentations and associated links
• Useful Web Sites
  • Bioinformatics sites
  • Programming sites for scientists
• Day 1: EC2, UNIX, and BLAST
  • Starting your cloud system
  • Logging into your new instance “in the cloud” (Mac version)
  • Logging into your Amazon machine (Windows version)
  • Installing dropbox on your EC2 machine
  • Installing and Running NCBI BLAST
  • Running a reciprocal BLAST
• Day 2: Mapping
  • Checking read quality with FastQC
  • Mapping reads with bwa and bowtie
• Day 3: Assembly
  • Short Read Assembly with Velvet
  • mRNAseq Assembly with Velvet & Oases
  • An Introduction to Unix
  • Handling Long Jobs in Unix
  • Storing data persistently with Amazon
• Day 4: Scripting & Stuff
  • An Introduction to Scripting
  • Some simple shell scripts to make your life easier
• Day 5: Statistics & Plotting
  • R Tutorial (part I)
  • Plotting Allele Frequencies with R
• Day 6: RNAseq Visualization
  • RNAseq mapping with Tophat
  • Building gene models using Cufflinks
  • Visualising RNAseq data & gene models
  • Gene differential expression using DEGseq
  • A simple mRNAseq analysis pipeline
• Day 7: ChIP-seq
  • Peak Predictions and Cis-regulatory Element Annotations
  • Interval operations with BEDtools
• Day 8: SNPs
  • Calling SNPs with Samtools

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