Six weeks sequence analysis bootcamp: (2015 Fall)

Week 1: Unix environment

  • Click to download the slides: Introduction to Unix (pdf)
  • Click to download the slides: Ghpcc (pdf)

Week 2: Genomic resources

  • Click to download the slides (pdf)

Week 3: RNA-Seq data processing

  • Click to download the slides (pdf)

Week 4: RNA-Seq Mapping

  • Click to download the slides (pdf)
  • Click to download the used R script
  • Click to the RNA-Seq mapping and quantification preperation (Excercise 1) (html)
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 Mapping and Quantification

  • Click to download the slides (pdf)
  • Click to the RNA-Seq transcriptome mapping and quantification tutorial (Excercise 2) (html)

Week 6: RNA-Seq Data Analysis

  • Click to download the slides (pdf)
  • Click to the RNA-Seq whole genome mapping (Excercise 3) (html)

Week 7: RNA-Seq data analysis using R

  • Please finish the tutorial before you come to the class below to start learning R
    tryr.codeschool.com
  • Click to the R tutorial for differential expression analysis with R (html)
  • Click to download R scripts(R)
  • Click to download extra R functions (R)
  • Click to download the data(tsv)