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  • Introduction
  • Library preparation
  • Experimental design
  • Analysis workflow
  • FASTQ format
  • Data repositories
  • Course data
  • Read QC and trimming
  • Read mapping
  • Mapping with STAR
  • Genome Browser
  • Mapping with Salmon
  • MultiQC report
  • Differential expression analysis
  • Functional analysis
  • Final project
  • Resources

    Resources

    DESeq2

    • Vignette
    • Tutorial

    References:

    1. https://en.wikipedia.org/wiki/Northern_blot
    2. https://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
    3. https://en.wikipedia.org/wiki/DNA_microarray
    4. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484.
    5. Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data
    6. Wingett SW, Andrews S. FastQ Screen: A tool for multi-genome mapping and quality control. Version 2. F1000Res. 2018 Aug 24
    7. Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182