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,

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

where i dont know how to seperate promoter &TSS , or is there need to seperate both is also confusing .

please help me with ur knowledge

Thank you

[rpolicastro]

What did you try?