I'm trying to use Homer to annotate peaks from the analysis in the Diffbind . I noticed recently that even when I'm assigning peaks as 0 or 1 (I don't have that information from the Diffbind) or forcing -strand plus or -strand minus, annotatePeaks.pl ignores the genes on the minus strand . For example, I have a peak with coordinates chr6 64295326 64295728 (hg38)
annotated as PHF3 by Homer, but in the UCSC genome browser it falls in the middle of EYS gene on the opposite strand, and PHF3 is far far away 649001 bp from it's promoter. I checked, that any of the genes annotated by Homer doesn't fall on the minus strand. I suppose that it's choosing the nearest tss but not taking into the account the length of the gene. How can I fix it to annotate all genes?
I'd be grateful for help
the command I'm using for annotating both strands:
annotatePeaks.pl MSC_Diffbind_both.bed hg38 > MSC_Diffbind_homer_anno_both.txt -go MSC_Diffbind_homer_GO_both -annStats MSC_Diffbind_homer_summary_both.txt -nmotifs -mdist -CpG -mbed MSC_Diffbind_motifs_both.bed -strand both