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2 days ago
Hi has anyone some experience with the use of ChromHMM for chromatin segmentation and can explain me how to get annotations for the generated chromatin states? I applied ChromHMM, that means the functions 'binarizeBed' and 'LearnModel', to a sample with three marks (H3K27ac,H3R8me2a,H4R3me2s) Is set the number of chromatin states to 8. The problem: How can I annotate my chromatin states with "active Promotor", "weak Enhancer" etc? In the LearnModel output, the eight states are simply numbered consecutively (E1-E8). how i can assign states as mentioned in reference plot. Thank YOu