Installation and Resources

Software

Bash Shell For this series, you will need access to the Bash shell. Linux and macOS users will have access to this already and should not need to install anything.

Windows users will need to do some extra work.

  • Install Git for Windows, which will provide acess to Bash shell and Git by following the instructions here.

RNA-seq processing workflow

In the final lesson, we will use miniconda to control in installation of several tools. Follow the steps below.

  1. Install miniconda using the appropriate directions from here: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html

  2. After closing and re-opening the terminal, the conda base environment should be enabled. To check this, make sure you see (base) to the left of your user name in the terminal prompt.

    (base) user: $

  3. Create a conda environment called rnaseq while installing the needed tools/software – enter “y” when prompted.

    conda activate base
conda create -n rnaseq -c bioconda fastqc trim-galore subread star

Data

Introductory Files These data are zipped and should begin downloading once the link below is clicked.

  • Click here to download the data.
  • Move the shell-lesson-data.zip file from your Downloads to your Desktop.
  • Unzip the file to extract the data. You should end up with a shell-lesson-data directory on your Desktop.

RNA-seq similated data/files For the last lesson, you will need simulated reads, fasta files, index files, etc.

  • Click here to download the data.
  • Move the directory to your Desktop if possible.