Hello, I've used ChromHMM with ChIP-seq aligment and identified some chromatin states of itnerest.
I am interested in the overlapping with other datasets to annotate them according to the segment they are located on. OverlapEnrichment seems exactly what I'm looking for, but I think I'm failing to interpret it correctly.
Running LearnModel with Chip-Seq aligments of two conditions, I get the expected segmentation (guess with staes based on both conditions). I then get two overlap enrichment plots, one per condition, for the dataset of regions I have provided. I have then overlapped using bedtools intersect the segmentation provided for each condition with my dataste of regions. The overlaps I'm getting don't make sense compared to the enrichment plots. For example, more than half of my regions overlap with a segment which is not enriched according to the figure.
Maybe I'm missing something, I'm asking in case someone has any experience. How could I get the segments corresponding to each region on my dataset?
Hope anyone has any comment on this. Thanks