Hello everyone, I am currently analyzing CUT&Tag data with ChromHMM and would appreciate some advice on model selection. Here is my setup : I have 8 histone marks 6 replicates treated and 6 replicates untreated, for both males and females.IGG controls are available for each batch. For now, I have generated two ChromHMM models, one for each sex, using the concatenated mode. For each model, I input all treated and untreated files together and the corresponding IGG controls. For each sex, I currently have:

• An emission matrix and transition matrix
• 6 segmentation/annotation files I then used these segmentation files with CSREP to identify chromatin state changes between untreated and treated conditions for both sexes, and compared the results within and between sexes.

is concatenated mode a good choice, or would another model better capture the differences between conditions?

Thank you in advance for your guidance!