Hi all, I've tried to annotate MACS2 ChIP-seq peaks using HOMER annotatePeaks.pl. I have just given to annotatePeaks.pl the annotation and the fasta files for my genome and it's working.
I'm not sure however about the column "Distance to TSS" on the annotation. The features I've given in the annotation are CDS, exon, 5' UTR, 3' UTR, gene, start codon, stop codon and transcript. I don't have TSSs specifically annotated. What's the reference HOMER is using for giving a number (and a sign, upstream or dowstream) in the "Distance to TSS" column? It migth be the ATG? I have failed to find this info on the documentation. And the distance would be from the middle of the peaks or the start/ending?
Hope anyone have any idea.
Thanks for your time.