Six weeks sequence analysis bootcamp:

Week 1: Unix environment

  • Click to download the slides (pdf)
  • Click to download the exercises (pdf)

Week 2: Databases, annotations, genomic resources

  • Click to download the slides (pdf)

Week 3: RNA-Seq data processing

  • Click to download the slides (pdf)
  • Click to access the exercises
  • Click to download the exercises (pdf)

Week 4: The Galaxy environment/UCSC genome browser

  • Click to download the slides (pdf)
  • Click to download the Galaxy slides (pdf)
Some example files
  • http://bioinfo.umassmed.edu/pub/data/filter/rRNA.fasta => Ribosomal RNAs
  • http://bioinfo.umassmed.edu/pub/data/mm10.fa => Genome reference
  • http://bioinfo.umassmed.edu/pub/data/test.fastq => Single end fastq example
  • http://bioinfo.umassmed.edu/pub/data/control_rep1.1.fq => Paired end fr
  • http://bioinfo.umassmed.edu/pub/data/control_rep1.2.fq => Paried end br

Week 5: RNA-Seq data processing/analysis using Galaxy and Dolphin

  • Click to download the slides (pdf)
  • Click to download the Galaxy slides (pdf)

Week 6: RNA-Seq data analysis using R

  • Please finish the tutorial before you come to the class below (8 section) to start learning R
    tryr.codeschool.com
  • Click to download the slides (pdf)
  • Click to download R scripts(R)
  • Click to see R scripts(html)