I am performing ChIP-Seq analysis of a transcription factor that binds as a dimer to palindromic sequences with variable gap in between. I need to align these motifs with different gap lengths back onto the genome in order to identify direct targets of the TF. In order to do this, I tried MEME-ChIP and Glam2 with default settings so far. I do see a palindromic motif in output which is quite similar to known motif. I can also see that the motif is a variable gapped by manual inspection.
But If I align this motif back to the genome using FIMO, I see many sequences at ChIP-peaks that match the motif but do not get picked up by FIMO.
Since there is a clear ChIP peak on these sequences and there is a clear motif sequence at the summit, I am baffled why such sites are not getting picked by genome alignment by FIMO. The sites picked by FIMO also show clear motifs indicating FIMO has worked too.
Am I missing something? Is there a better tool or different way to work with gapped motifs? Thanks for your help!
P.S. I have also tried SICER for gapped motifs.