I generated intergenic and intron BED files by following along with Steven’s notebooks:
Steven intergenic BED file notebook (GitHub):
Steven intron BED file notebook (GitHub):
Here’s how I generated these two BED files.
Jupyter Notebook (GitHub):
Intergenic BED file (BED):
Intron BED file (BED):
Will add these files to the OSF repository for this project.
Here’s how they look in IGV: