Hi,
I actually try to run ChromHMM on a new cell line for which I have the following markers (H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, H3K36me3, Dnase Hotspot and input) and I have some difficulties to retrieve right annotation corresponding to different chromatin state. Does somebody have some advices/tips to share?
Does somebody already try this software on a new cell line?
Thanks in advance,
Can you clarify "retrieve the right annotation"? Are you asking about where to get more data, or are you asking about how to interpret the ChromHMM output?
Hi,
Sorry for the misunderstood, i was talking about how to interpret the ChromHMM output and more specially how do you assess the right annotation for each state.