Prerequisites

The course is intended for those who have basic familiarity with Unix and the R scripting language.

• If a refresher is needed for Unix command line (hopefully not), please go over this tutorial and its companion cheatsheet.
• Another helpful UNIX cheatsheet: here
• Getting down to basics: an introduction to the fundamentals of R (courtesy of Mark Ravinet).
• Gentle introduction to R/Biocondutor: here
• For a full in-depth guide of Bioconductor ecosystem: read the comprehensive R/Bioconductor book from Kasper D. Hansen available under the CC BY-NC-SA 4.0 license. It is freely available under the CC BY-NC-SA 4.0 license: Link to EPUB

Local configuration

• Computer with high-speed internet access

• Zoom visioconference software

• For Windows users: PLEASE INSTALL WSL 2. Instructions are here: learn.microsoft.com/en-us/windows/wsl/install

• IGV software installed

• Several system dependencies

  • R>=4.1: https://cloud.r-project.org/
  • fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • cutadapt: https://cutadapt.readthedocs.io/en/stable/installation.html
  • trim_galore: https://github.com/FelixKrueger/TrimGalore
  • bowtie2: https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#obtaining-bowtie-2
  • deepTools: https://deeptools.readthedocs.io/en/develop/content/installation.html
  • macs2: https://github.com/macs3-project/MACS/wiki/Install-macs2#easy-installation-through-pypi
  • meme: https://meme-suite.org/meme/doc/install.html?man_type=web
  • subread: https://subread.sourceforge.net/

Installing system dependencies with micromamba

micromamba is a blazing-fast flavour of conda, a software manager available in Mac and Linux. micromamba sets up environments, directories in your computer in which micromamba installs softwares only available upon environment activation.

To install micromamba and system dependencies listed hereabove, use the following:

sh

# apt update && apt install -y bzip2 curl wget
curl micro.mamba.pm/install.sh | bash
bash
micromamba create -n epigenomics
micromamba activate epigenomics
micromamba install -c bioconda -c conda-forge \
    fastqc fastqc trim-galore bowtie2 deepTools macs2 meme subread star samtools bedtools \
    mawk tree java-jdk ucsc-bedGraphToBigWig \
    pandas numpydoc matplotlib cooler cooltools hicstuff

• Several R packages, the main ones being:

  • BiocManager
  • SummarizedExperiment
  • rtracklayer
  • GenomicRanges
  • GenomicAlignments
  • GenomicFeatures
  • DESeq2
  • gprofiler2