Short read quality evaluation and trimming

Etherpad here

GitHub Repo here

• Getting started
  • Local installs and Web site
  • Software we’ll be using on the server
  • A first test
• Some background
  • What do we use Illumina sequencing for?
  • Basic Recommendations:
  • Structure of a FASTQ file
• Evaluating samples with FastQC
  • Download some data
  • Running fastqc
• Trimming reads with Trimmomatic
  • E. coli trimming
  • Trimming the yeast RNAseq data
• Evaluating read mismatch statistics: mapping and de novo
  • Looking at read mismatch profiles by mapping to a reference
  • Looking at the read mismatch profile de novo
• Final thoughts on short-read trimming
  • A summary of recommendations
  • Some references

Indices and tables

• Index
• Module Index
• Search Page

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