GenomicLinks is a computational tool designed to predict chromatin interactions in Zea mays (maize). It utilizes genomic data to analyze and predict the interactions between different regions of chromatin, aiding researchers in understanding gene regulation and genome architecture in maize.

Before you begin, ensure you have met the following requirements:

• You have installed the latest version of Miniconda.
• You have a Windows, Linux, or macOS machine.

To install GenomicLinks, follow these steps:

1. Clone the repository: Clone the GenomicLinks repository to your local machine using git:

   git clone https://github.com/jlab-code/GenomicLinks.git
   cd GenomicLinks
   

2. Setup Conda environmnet: Create and activate conda env.

   conda env create -f jup.yml
   conda activate jup
   

3. Download Reference Genome: Download the Zea mays reference genome fasta file. Ensure you place it in the appropriate directory or update the script paths to its location. Reference genome files can typically be found at:
   • NCBI Zea mays
   • Ensembl Plants for Zea mays

1. Run the master script 0_runGenomicLinks.sh to process all steps automatically:

   sh 0_runGenomicLinks.sh
   

Make sure all paths in the script are correctly set to match your directory structure and data files.

2. Individual Script Execution: You can also run each script individually if you need more control over the execution or for debugging purposes:

   python3 1_PreprocessBEDPE.R "/path/to/your/bedpe/file" "/path/to/your/scripts_directory/prediction_output" #Processes the BEDPE file and prepares data.
   python3 2_ExtractRegion.py "/path/to/your/scripts_directory/prediction_output" "/path/to/fasta/file" #Extracts regions from the genome.
   python3 3_Prediction.py "/path/to/your/scripts_directory/prediction_output" "/path/to/your/scripts_directory/weights-improvement-dp2500-58.hdf5 "#Performs the prediction of chromatin interactions.
   python3 4_MergePredictionResults.sh "/path/to/your/scripts_directory/prediction_output" #Merges all individual prediction files into a final result.
   
   

Ensure you provide the necessary arguments and paths when running each script individually.

For easier access and usage, visit genomiclinks.com where you can use GenomicLinks through a user-friendly web interface.

If you want to contact me you can reach me at <[email protected]>.