Tfe1 and Tfe2 toxin expression in S. cerevisiae RNA-seq

Collaborators: Katharina Trunk

Usage

On a Linux cluster

Create and activate a conda environment

cd rna_seq
conda create --name yeast_tfe --file env.txt
conda activate yeast_tfe

Make sure FASTQ files are in the ./fastq subdirectory.

Run snakemake

./run_snake.sh

This will trim adapters, perform quality control, download genome files, map reads to the reference and count reads per gene.

In RStudio

Once snakemake is finished, we suggest using RStudio. If this is done on a different machinge (I run RStudio on a laptop), some data need to be copied over (see ./get_data.sh and ./rsync_include.txt). Once in RStudio, start in the top project directory. The first step is to create environment using renv:

install.packages("renv")
renv::restore()

This will install all necessary packages. Run the targets pipeline.

targets::tar_make()

This will carry out all the calculations, create figures (some as targets, some in ./fig directory) and output TSV files in directory ./tab.