How to map query coordinates on to genome gff annotation files ?

Question

[isha.lily20]

Hello Researchers

I have a project where I got stuck on: mapping query coordinates on to gff annotation files

It means I have to find all the total counts of gene, mRNA, exon, CDS, 3'-utr, 5'-utr, promoter, intergenic, intron, Transposable elements?

I tried homer annotatePeaks.pl where I got only intergenic, exons, TTS & promoter-TSS(combined)?

Used this command:

annotatePeaks.pl <peak file | tss> <genome version>  [additional options...]

where I don't know how to separate promoter & TSS, or is there need to separate both is also confusing.

Please help me with your knowledge

Thank you

[rpolicastro]

What did you try?