DNA methylation EPIC array and ChromHMM

Question

[macsuejacques]

Hello,

I have DNA methylation data obtained by the EPIC array and I would like to use this data to check for chromatin states using the ChroHMM software. I understand that the data must be in a binary format, grouped by each 200bp, and separated by chromosome. I have been thinking and searching and I cannot come up with a solution on how to make my data binary and grouped each 200bp. Note that the whole chromosome is not sequenced by this technology, so i would have to group each 200 but regions without CpGs will need to receive a value of 2. Is there a package that can help me do that? Or has anyone done this before? Please any help would be appreciated!

[anikb]

Were you able to figure something out? Using EPIC data with chromHMM is something I am intererested in too, but can't find an the use of EPIC with chromHMM anywhere. Do you have any reference or papers that discuss using EPIC array to get chromatin states?

[macsuejacques]

not yet. I got some papers that have done something similar but I haven't figured it out as yet.

Answer 1

[Lluís R.]

I think you will need to use the BinarizedBed or BinarizeBam command of ChromHMM