Promoter regions and visualization on IGV

Question

[abhay.kanodia]

Hello, I am very new to ATAC-seq data and IGV, I want to know when you type in the genes, it only shows introns and exons. How do I visualize the promoter region? For example, I have gene IGFBP5. How to include the promoter region. Thank you!

Answer 1

[ATpoint]

Promoters are not annotated in GTF files as their boundaries are not precisely defined and probably celltype-specific. People usually use like 500-1kb upstream of a TSS to approximate them. You could make a BED file with these coordinates based on a GTF file or just highlight it in IGV manually for a few genes.

[abhay.kanodia]

Thank you very much ATPoint