README file for operation of the code used in Barshad et al 2018 Genome Research

1. Please use the "Main_pipeline_Barshad 2018.bsh" file to execute the main code. This file should be run in a LINUX system, and will make use of all other files in the folder.
The code requires a PYTHON 3 platform.

2. The user should create an output folder for the results, and write the correct address in line "outputDir=$1" of the main code.

3. The user requires downloading the following file from the GTex portal: GTEx_Analysis_v6p_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct

Here is the address for the download process: https://www.gtexportal.org/home/datasets

4. After downloading the file please change lines 2-5 to connect the downloaded file to the code and other files in the folder.

5. The code and associated files could be also downloaded from: https://github.com/dmishmar/Barshad_2018