making annotation files

[aciernia]

This isn't a GAT issue so much as a clarification on how to build annotation files for use with gat-great. I would like to build an annotation for Hg38 but am struggling to get the 1MB extension that GREAT uses. Here is what I have tried so far:

1. download TSS coordinates from Ensemble for Hg38 (including chromosome, TSS, geneid, and strand)
2. Add 5kb downstream and 1kb downstream of each TSS using bedtools flank with strand = basal region
3. Add 1MB up and downstream of the basal region using bedtools slop with strand
   But now I am stuck as to how to remove the overlapping regions. There must be a better approach for extending the regions 1MB until they hit the next basal region?? Or if there is a script for building these types of annotations it would be awesome if you were willing to share!

Thanks!

Annie