Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad peaks?

Question

[Melinda]

Hi!

I am using publicly available data for chromatin state annotation, and building my model with chromHMM. You need to send in an application in order to get the raw data (fastq files), but the enriched regions (peak regions) are freely available. My plan is to build a model using these freely available peaks with binarizeBed -peaks, however, according to the manual, this is not recommended for broad peaks. Could someone tell me why that is? How would it affect the annotation?

Thank you for any advice, and have a great one!

Answer 1

[sarah.hazell.pickering]

Hi! As best I can tell from their paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945550/) the broad peaks are not suitable because they tend to be larger than the default chromHMM operating resolution of 200bp.

[e.r.zakiev]

that makes sense