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