#ENCODE to Ecosystem Data Hub converter These scripts fetch ENCODE metadata from the ENCODE portal, and output it in the Ecosystem Data Hub JSON format. Use fetch_all_exp_jsons.py to download datasets for all experiments, or individual experiment scripts.

Usage

Parameters

• assembly: Assembly name (e.g. hg19, GRCh38, mm10)
• taxon-id: Species taxonomy id (e.g. 9606 for human, 10090 for mouse)

Example

cd IHEC_json_converter
python ./fetch_all_exp_jsons.py --assembly=hg19 --taxon-id=9606

Credits

Original development by ENCODE team, available here: https://github.com/kpaskov/PaskovEncodeScripts