1000_genes_ecoli

This is the Github Repository for the whole genome Reg-Seq project. The code in this project is written in Julia, which can be downloaded here.

Setting up Computational Environment

Julia

To run the code in this project, you need to activate the custom environment, which can be done by starting Julia in this project folder. This can either be done by adding the Julia path as an Environment variable, or by starting the executable Julia file and navigating into the project folder (using the shell mode by typing ;, shell mode can be left by pressing esc). Instructions on how Julia can be started from the command line can be found here. Once the correct folder is selected, the working environment can be set by first entering package mode (pressing ]) typing in the Julia REPL

julia> activate .

Once the environment is activated, all necessary packages can be installed with

julia> instantiate

Package mode can be left again by typing pressing esc.

To run a script use

julia> include("path/to/script.jl")

Conda

During processing of sequencing data, we use the software package fastp. This software can be installed using conda, therefore we need to set up an appropriate conda environment. We provide a suitable conda environment that was used to run the processing for this project. The environment can be installed by running

conda env create -f environment.yml

Subsequently, the environment needs to be activated in order to be used. This can be done by

conda activate wgregseq

For sequence processing we use fastp (version 0.23.2). This software is a command line tool that can be installed with conda. We provide a minimal conda environment called fastp which can be installed with

conda env create -f fastp_environment.yml

from this directory.

BBmap

During processing of sequencing data, we use bbmap. It can be downloaded and used straight away. BBmap requires a working Java installation on the machine. Replace the bbmap folder in this repository with the unpacked folder that you downloaded for bbmap. bbmap requires a working Java installation, so make sure that you have one.

Installation check

Finally, to make sure everything is installed correctly, run check_installation.sh. It will prompt you with installation requests if an essential piece of software is missing.

Repository structure

code

Contains all code files used to design experiments, process and analyze data and create figures. Look in here to reproduce the results of the paper.

src

Contains the custom Julia software module.

notebooks

Contains explanatory notebooks that walk through certain steps in the experimental design and data processing.

test

Contains tests for software module.

data

Contains supplementary data files.