I am doing an analysis in which I am interested in knowing the orientation of the CTCF motif at certain positions in the genome. For this I have used the program findMotifsGenome.pl with the file CTCF.motif from the Homer database. However, I noticed that the motif that Homer reports as forward is the one that Jaspar and other papers report as reverse complementary and vice versa. I have found that with other motifs (such as YY1) this does not happen, so I think there must be an error in Jaspar or Homer. It's important for me because I am interested in catching pairs of convergent motifs and this selection is directly affected by the motif orientation. Has anyone noticed this?
Thank you very much,