I used HOMER annotatePeaks.pl to annotate my peaks.
Here is the format for my code:
annotatePeaks.pl peak.bed ref.fa -gff3 ref.gff3 > PeakAnno.txt.
But, I don't know why it is "NA" for the columns of "Focus Ratio/Region Size" and Detailed Annotation""? I am more interested in the "Detailed Annotation".
Really hope I can get it fixed here. Is it the problem with my code or my annotation file? I did not get answer from the manual http://homer.ucsd.edu/homer/ngs/annotation.html and any threads neither.
Thank you so much!