MMG434
  • Install software and use FileZilla to transfer files
    • Software to install:
    • Using FileZilla to transfer files:
    • R
    • RStudio
    • Qualimap
    • Transferring files from your machine to the HPCC using FileZilla
  • RNA-seq background information, basic Linux/Unix commands, Trimmomatic, and FastQC
    • RNA-seq background information
    • Basic Linux/Unix commands
    • Getting some RNA-seq data
    • Trimmomatic
    • FastQC
    • Automating all of this
  • Align sequences with Bowtie and count gene features with HTSeq
    • Bowtie
    • HTSeq
  • Analyzing L. reuteri data
  • Modification to the scripts from today (3-4-15)!
  • Differential gene expression analysis with edgeR
    • Download and install edgeR
    • Read in the data to RStudio
    • Group the data together
    • Filter out low counts
    • Regroup and normalize the libraries
    • See how samples separate by treatment
    • Differential expression calculations
    • Plot the results
  • FastQC files
  • License
  • Questions?
 
MMG434
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© Copyright 2015, Benjamin K Johnson.

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