I am running Homer annotatePeaks.pl to assign my ATAC-seq peaks to genes. For the annotation, I am using a custom Ensembl GTF file and a custom Ensembl TSS file.
annotatePeaks.pl peaks.txt hg38 -gtf Ensembl_hg38.gtf -cTSS Ensembl_hg38.tss > annotated_peaks.txt
When using a custom GTF file, the Homer guidance states that "It will also use the GTF file's definition of TSS/TTS/exons/Introns for Basic Genome Annotation."
I was wondering what column of an Ensembl GTF file would be used for this? Does Homer work out which regions are intronic, intergenic etc. based on the regions that are assigned as exons or start_codons in field 3 of the GTF file, as I can't find any regions that are explicitly assigned as introns or intergenic regions?