Running EDNAtran with Aspergillus flavus as a model system.

Contents [TOC]

This repository contains all the scripts that allowed to obtain 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

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