Running EDNAtran with Aspergillus flavus as a model system.

Contents

This repository contains some scripts that allowed to validate all the 231 e-probes associated with aflatoxin production in AF70. There are multiple steps associated with the design of e-probes. In this case, all the methodology is explained in our manuscript.

To start replicating the results of our manuscript first clone the repository as follows:

git clone https://github.com/andrese52/EDNAtran.git
cd EDNAtran

Dependencies

• Mummer 3.9.4 alpha: Installed following these instructions

• Bioperl Search module

  cpan Bio::SearchIO
  

• Circos

  wget http://circos.ca/distribution/circos-0.69-6.tgz
  tar xvfz circos-0.69-6.tgz
  cd circos-0.69-6
  

  • Some perl modules are required by circos and can be installed as follows:

  sudo apt-get install libgd-perl
  cpan Config::General
  cpan GD::Polyline
  cpan Math::Bezier
  cpan Math::Round
  cpan Readonly
  cpan Params::Validate
  cpan Math::VecStat
  cpan Statistics::Basic
  cpan Regexp::Common
  cpan Text::Format
  cpan Set::IntSpan
  

  However, it depends on your OS, in other cases you might need to install more or less modules. This was our specific case. We are using Ubuntu 18.04.

  • You can also download the examples folder to practice from here Then add the bin folder to your permanent $PATH

• gnu-plot

   sudo apt install gnuplot-x11
  

Setting up environmental variables

We need to tell our computer where to find the scripts. Therefore we must run this code once we have cloned the repository:

export PATH=$PATH:$(pwd)/scripts

E-probe coordinates

Retrieving coordinates from different aflatoxin gene clusters. First we need to retrieve all the aflatoxin gene clusters available on NCBI. First move to the results folder and run the following command

cd results
bash ../scripts/run_circos.sh ../gene-cluster-IDs.txt